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Rivera-Silva R, Chávez Montes RA, Cervera A, Jaimes-Miranda F. Proposal of Reference Genes for Tomato Fruit Ripening qRT-PCR Data Normalization. PLANT & CELL PHYSIOLOGY 2024; 65:1083-1086. [PMID: 38706155 DOI: 10.1093/pcp/pcae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 04/19/2024] [Accepted: 04/30/2024] [Indexed: 05/07/2024]
Affiliation(s)
- Ricardo Rivera-Silva
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), Camino a la Presa San José 2055, San Luis Potosí 78216, México
| | | | - Alejandra Cervera
- Genómica Computacional, Instituto de Medicina Genómica (INMEGEN), Periferico Sur 4809, Mexico City 14610, México
| | - Fabiola Jaimes-Miranda
- CONAHCyT-IPICYT/División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, San Luis Potosí 78216, México
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2
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Jagannathan NS, Koh JYP, Lee Y, Sobota RM, Irving AT, Wang LF, Itahana Y, Itahana K, Tucker-Kellogg L. Multi-omic analysis of bat versus human fibroblasts reveals altered central metabolism. eLife 2024; 13:e94007. [PMID: 39037770 PMCID: PMC11262796 DOI: 10.7554/elife.94007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/07/2024] [Indexed: 07/23/2024] Open
Abstract
Bats have unique characteristics compared to other mammals, including increased longevity and higher resistance to cancer and infectious disease. While previous studies have analyzed the metabolic requirements for flight, it is still unclear how bat metabolism supports these unique features, and no study has integrated metabolomics, transcriptomics, and proteomics to characterize bat metabolism. In this work, we performed a multi-omics data analysis using a computational model of metabolic fluxes to identify fundamental differences in central metabolism between primary lung fibroblast cell lines from the black flying fox fruit bat (Pteropus alecto) and human. Bat cells showed higher expression levels of Complex I components of electron transport chain (ETC), but, remarkably, a lower rate of oxygen consumption. Computational modeling interpreted these results as indicating that Complex II activity may be low or reversed, similar to an ischemic state. An ischemic-like state of bats was also supported by decreased levels of central metabolites and increased ratios of succinate to fumarate in bat cells. Ischemic states tend to produce reactive oxygen species (ROS), which would be incompatible with the longevity of bats. However, bat cells had higher antioxidant reservoirs (higher total glutathione and higher ratio of NADPH to NADP) despite higher mitochondrial ROS levels. In addition, bat cells were more resistant to glucose deprivation and had increased resistance to ferroptosis, one of the characteristics of which is oxidative stress. Thus, our studies revealed distinct differences in the ETC regulation and metabolic stress responses between human and bat cells.
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Affiliation(s)
- N Suhas Jagannathan
- Cancer and Stem Cell Biology Programme, Duke-NUS Medical SchoolSingaporeSingapore
- Centre for Computational Biology, Duke-NUS Medical SchoolSingaporeSingapore
| | - Javier Yu Peng Koh
- Cancer and Stem Cell Biology Programme, Duke-NUS Medical SchoolSingaporeSingapore
| | - Younghwan Lee
- Cancer and Stem Cell Biology Programme, Duke-NUS Medical SchoolSingaporeSingapore
| | - Radoslaw Mikolaj Sobota
- Functional Proteomics Laboratory, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and ResearchSingaporeSingapore
| | - Aaron T Irving
- Programme in Emerging Infectious Diseases, Duke-NUS Medical SchoolSingaporeSingapore
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang UniversityHainingChina
| | - Lin-fa Wang
- SingHealth Duke-NUS Global Health InstituteSingaporeSingapore
| | - Yoko Itahana
- Cancer and Stem Cell Biology Programme, Duke-NUS Medical SchoolSingaporeSingapore
| | - Koji Itahana
- Cancer and Stem Cell Biology Programme, Duke-NUS Medical SchoolSingaporeSingapore
| | - Lisa Tucker-Kellogg
- Cancer and Stem Cell Biology Programme, Duke-NUS Medical SchoolSingaporeSingapore
- Centre for Computational Biology, Duke-NUS Medical SchoolSingaporeSingapore
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3
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Li X, Xiao H, Zhu L, Liu Q, Zhang B, Wang J, Wu J, Song Y, Wang S. Rank-In Integrated Machine Learning and Bioinformatic Analysis Identified the Key Genes in HFPO-DA (GenX) Exposure to Human, Mouse, and Rat Organisms. TOXICS 2024; 12:516. [PMID: 39058168 PMCID: PMC11280914 DOI: 10.3390/toxics12070516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/04/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024]
Abstract
Hexafluoropropylene Oxide Dimer Acid (HFPO-DA or GenX) is a pervasive perfluorinated compound with scant understood toxic effects. Toxicological studies on GenX have been conducted using animal models. To research deeper into the potential toxicity of GenX in humans and animals, we undertook a comprehensive analysis of transcriptome datasets across different species. A rank-in approach was utilized to merge different transcriptome datasets, and machine learning algorithms were employed to identify key genetic mechanisms common among various species and humans. We identified seven genes-TTR, ATP6V1B1, EPHX1, ITIH3, ATXN10, UBXN1, and HPX-as potential variables for classification of GenX-exposed samples, and the seven genes were verified in separate datasets of human, mouse, and rat samples. Bioinformatic analysis of the gene dataset further revealed that mitochondrial function and metabolic processes may be modulated by GenX through these key genes. Our findings provide insights into the underlying genetic mechanisms and toxicological impacts of GenX exposure across different species and offer valuable references for future studies using animal models to examine human exposure to GenX.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Shuo Wang
- Tianjin Key Laboratory of Food Science and Health, Research Institute of Public Health, School of Medicine, Nankai University, No.94 Weijin Road, Tianjin 300071, China; (X.L.); (H.X.); (L.Z.); (Q.L.); (B.Z.); (J.W.); (J.W.); (Y.S.)
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4
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Yuan Y, Xu Q, Wani A, Dahrendorff J, Wang C, Shen A, Donglasan J, Burgan S, Graham Z, Uddin M, Wildman D, Qu A. Differentially expressed heterogeneous overdispersion genes testing for count data. PLoS One 2024; 19:e0300565. [PMID: 39018275 PMCID: PMC11253971 DOI: 10.1371/journal.pone.0300565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 02/29/2024] [Indexed: 07/19/2024] Open
Abstract
The mRNA-seq data analysis is a powerful technology for inferring information from biological systems of interest. Specifically, the sequenced RNA fragments are aligned with genomic reference sequences, and we count the number of sequence fragments corresponding to each gene for each condition. A gene is identified as differentially expressed (DE) if the difference in its count numbers between conditions is statistically significant. Several statistical analysis methods have been developed to detect DE genes based on RNA-seq data. However, the existing methods could suffer decreasing power to identify DE genes arising from overdispersion and limited sample size, where overdispersion refers to the empirical phenomenon that the variance of read counts is larger than the mean of read counts. We propose a new differential expression analysis procedure: heterogeneous overdispersion genes testing (DEHOGT) based on heterogeneous overdispersion modeling and a post-hoc inference procedure. DEHOGT integrates sample information from all conditions and provides a more flexible and adaptive overdispersion modeling for the RNA-seq read count. DEHOGT adopts a gene-wise estimation scheme to enhance the detection power of differentially expressed genes when the number of replicates is limited as long as the number of conditions is large. DEHOGT is tested on the synthetic RNA-seq read count data and outperforms two popular existing methods, DESeq2 and EdgeR, in detecting DE genes. We apply the proposed method to a test dataset using RNAseq data from microglial cells. DEHOGT tends to detect more differently expressed genes potentially related to microglial cells under different stress hormones treatments.
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Affiliation(s)
- Yubai Yuan
- Department of Statistics, The Pennsylvania State University, State College, PA, United States of America
| | - Qi Xu
- Department of Statistics, University of California Irvine, Irvine, CA, United States of America
| | - Agaz Wani
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, United States of America
| | - Jan Dahrendorff
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, United States of America
| | - Chengqi Wang
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, United States of America
| | - Arlina Shen
- University of California Berkeley, Berkeley, CA, United States of America
| | - Janelle Donglasan
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, United States of America
| | - Sarah Burgan
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, United States of America
| | - Zachary Graham
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, United States of America
| | - Monica Uddin
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, United States of America
| | - Derek Wildman
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, United States of America
| | - Annie Qu
- Department of Statistics, University of California Irvine, Irvine, CA, United States of America
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5
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Wu J, Liu F, Jiao J, Luo H, Fan S, Liu J, Wang H, Cui N, Zhao N, Qu Q, Kuraku S, Huang Z, Xu L. Comparative genomics illuminates karyotype and sex chromosome evolution of sharks. CELL GENOMICS 2024:100607. [PMID: 38996479 DOI: 10.1016/j.xgen.2024.100607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/01/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024]
Abstract
Chondrichthyes is an important lineage to reconstruct the evolutionary history of vertebrates. Here, we analyzed genome synteny for six chondrichthyan chromosome-level genomes. Our comparative analysis reveals a slow evolutionary rate of chromosomal changes, with infrequent but independent fusions observed in sharks, skates, and chimaeras. The chondrichthyan common ancestor had a proto-vertebrate-like karyotype, including the presence of 18 microchromosome pairs. The X chromosome is a conversed microchromosome shared by all sharks, suggesting a likely common origin of the sex chromosome at least 181 million years ago. We characterized the Y chromosomes of two sharks that are highly differentiated from the X except for a small young evolutionary stratum and a small pseudoautosomal region. We found that shark sex chromosomes lack global dosage compensation but that dosage-sensitive genes are locally compensated. Our study on shark chromosome evolution enhances our understanding of shark sex chromosomes and vertebrate chromosome evolution.
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Affiliation(s)
- Jiahong Wu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Fujiang Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jie Jiao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Haoran Luo
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China; Key Laboratory of Ministry of Education for the Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, China
| | - Shiyu Fan
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jiao Liu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Hongxiang Wang
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Ning Cui
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Ning Zhao
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China; Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Qingming Qu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shigehiro Kuraku
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Shizuoka, Japan; Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Japan
| | - Zhen Huang
- Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, Fuzhou 350108, China
| | - Luohao Xu
- Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, MOE Key Laboratory of Freshwater Fish Reproduction and Development, School of Life Sciences, Southwest University, Chongqing 400715, China.
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6
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Diez JFF, Tegeler AP, Flesher CG, Michelotti TC, Ford H, Hoque MN, Bhattarai B, Benitez OJ, Christopher GF, Strieder-Barboza C. Extracellular matrix modulates depot-specific adipogenic capacity in adipose tissue of dairy cattle. J Dairy Sci 2024:S0022-0302(24)00985-8. [PMID: 38969002 DOI: 10.3168/jds.2024-25040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 06/10/2024] [Indexed: 07/07/2024]
Abstract
Adipose tissue (AT) expands through both hyperplasia and hypertrophy. During adipogenesis, adipose stromal and progenitor cells (ASPCs) proliferate and then accumulate lipids, influenced by the local AT microenvironment. Increased adipogenic capacity is desirable as it relates to metabolic health, especially in transition dairy cows where excess free fatty acids in circulation can compromise metabolic and immune health. Our aim was to elucidate the depot-specific adipogenic capacity and ECM properties of subcutaneous (SAT) and visceral (VAT) AT of dairy cows and define how the ECM affects adipogenesis. Flank SAT and omental VAT samples were collected from dairy cows in a local abattoir. Tissue samples were utilized for transcriptome analysis, targeted RT-qPCR for adipogenic markers, adipocyte sizing, assessment of viscoelastic properties and collagen accumulation, and then decellularized for native ECM isolation. For in vitro analyses, SAT and VAT samples were digested via collagenase, and ASPCs cultured for metabolic analysis. Adipogenic capacity was assessed by adipocyte size, quantification of ASPCs in stromal vascular fraction (SVF) via flow cytometry, and gene expression of adipogenic markers. In addition, functional assays including lipolysis and glucose uptake were performed to further characterize SAT and VAT adipocyte metabolic function. Data were analyzed using SAS (version 9.4; SAS institute Inc., Cary, NC) and GraphPad Prism 9. Subcutaneous AT adipogenic capacity was greater than VAT's, as indicated by increased ASPCs abundance, increased magnitude of adipocyte ADIPOQ and FASN expression during differentiation, and higher adipocyte lipid accumulation as shown by an increased proportion of larger adipocytes and abundance of lipid droplets. Rheologic analysis revealed that VAT is stiffer than SAT, which led us to hypothesize that differences between SAT and VAT adipogenic capacity were partly mediated by depot-specific ECM microenvironment. Thus, we studied depot-specific ECM-adipocyte crosstalk using a 3D model with native ECM (decellularized AT). Subcutaneous AT and VAT ASPCs were cultured and differentiated into adipocytes within depot-matched and mis-matched ECM for 14d, followed by ADIPOQ expression analysis. Visceral AT ECM impaired ADIPOQ expression in SAT cells. Our results demonstrate that SAT is more adipogenic than VAT and suggest that divergences between SAT and VAT adipogenesis are partially mediated by the depot-specific ECM microenvironment.
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Affiliation(s)
- J F Fiallo Diez
- Department of Veterinary Sciences, Texas Tech University, Lubbock, TX
| | - A P Tegeler
- Department of Veterinary Sciences, Texas Tech University, Lubbock, TX
| | - C G Flesher
- Department of Medicine, University of Pennsylvania, Philadelphia, PA
| | - T C Michelotti
- Department of Veterinary Sciences, Texas Tech University, Lubbock, TX
| | - H Ford
- Department of Veterinary Sciences, Texas Tech University, Lubbock, TX
| | - M N Hoque
- Department of Mechanical Engineering, Texas Tech University, Lubbock, TX
| | - B Bhattarai
- Department of Mechanical Engineering, Texas Tech University, Lubbock, TX
| | - O J Benitez
- Department of Veterinary Sciences, Texas Tech University, Lubbock, TX; School of Veterinary Medicine, Texas Tech University, Amarillo, TX
| | - G F Christopher
- Department of Mechanical Engineering, Texas Tech University, Lubbock, TX
| | - C Strieder-Barboza
- Department of Veterinary Sciences, Texas Tech University, Lubbock, TX; School of Veterinary Medicine, Texas Tech University, Amarillo, TX.
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7
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Gao H, Tian Y, Zhang H, Li Y, Li C, Li B. Species-specific duplicated FMRFaR-like gene A62 regulates spontaneous locomotion in Apolygus lucorum. PEST MANAGEMENT SCIENCE 2024; 80:3358-3368. [PMID: 38385791 DOI: 10.1002/ps.8039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/05/2024] [Accepted: 02/22/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND Apolygus lucorum, a major cotton pest, has undergone a significant expansion of the FMRFaR gene within the GPCR superfamily, resulting in two classes of GPCR, namely FMRFaR (A54-55) and newly duplicated FMRFaR-like (A56-62). Notably, FMRFaR-like genes, particularly A62, show enhanced expression in the legs and wings of adults, indicating their potential role in locomotion. Employing A62 as a representative of FMRFaR-like, our study investigates the influence of FMRFa, FMRFaR, and FMRFaR-like on locomotion and development of A. lucorum. RESULTS FMRFaR and FMRFa exhibit comparable temporal and tissue expression patterns, whereas the FMRFaR-like genes within A. lucorum exhibit completely distinct evolutionary and expression patterns compared to classical FMRFaR. RNA interference (RNAi) experiments revealed that suppressing FMRFa expression results in complete lethality in A. lucorum, but neither FMRFaR nor A62 exhibit the same effect after RNAi. Suppressing the expression of FMRFa only decreases the expression of the A54 gene simultaneously, suggesting that A54 may function as a classical FMRFaR activated by FMRFa. RNAi of A62 leads to wing malformation and a significant reduction in spontaneous movement behavior in A. lucorum. Further transcriptomic analysis revealed that A62 affects the A. lucorum's movement behavior through energy metabolism pathways and motor protein pathways. CONCLUSION Our study unveils the unique and complex roles of FMRFa and its receptor in A. lucorum. These findings provide valuable insights into potential targets for pest control strategies aimed at managing A. lucorum populations in cotton fields. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Han Gao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Ying Tian
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Hui Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yanxiao Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Chenjun Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Bin Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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8
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Etzel L, Apsley AT, Hastings WJ, Ye Q, Shalev I. Early life adversity is associated with differential gene expression in immune cells: A cluster-based analysis across an acute psychosocial stressor. Brain Behav Immun 2024; 119:724-733. [PMID: 38663776 PMCID: PMC11190835 DOI: 10.1016/j.bbi.2024.04.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/19/2024] [Accepted: 04/22/2024] [Indexed: 05/05/2024] Open
Abstract
Elucidating mechanisms by which early-life adversity (ELA) contributes to increased disease risk is important for mitigating adverse health outcomes. Prior work has found differences in immune cell gene expression related to inflammation and mitochondrial activity. Using a within-person between-group experimental design, we investigated differences in gene expression clusters across acute psychosocial stress and no-stress conditions. Participants were young adults (N = 29, aged 18 - 25 years, 62 % female, 47 % with a history of ELA). Gene expression was assessed in peripheral blood mononuclear cells collected at 8 blood draws spanning two 5-hour sessions (stress vs. no-stress) separated by a week, 4 across each session (number of observations = 221). We applied two unsupervised gene clustering methods - latent profile analysis (LPA) and weighted gene co-expression analysis (WGCNA) - to cluster genes with similar expression patterns across participants. LPA identified 11 clusters, 7 of which were significantly associated with ELA-status. WGCNA identified 5 clusters, 3 of which were significantly associated with ELA-status. LPA- and WGCNA-identified clusters were correlated, and all clusters were highly preserved across sessions and time. There was no significant effect of acute stress on cluster gene expression, but there was a significant effect of time, and significant differences by ELA-status. ELA-associated clusters related to RNA splicing/processing, inflammation, leukocyte differentiation and division, and mitochondrial activity were differentially expressed across time: ELA-exposed individuals showed decreased expression of these clusters at 90-minutes while controls showed increased expression. Our findings replicate previous work in this area and highlight additional mechanisms by which ELA may contribute to disease risk.
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Affiliation(s)
- Laura Etzel
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
| | - Abner T Apsley
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
| | - Waylon J Hastings
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA; Department of Psychiatry and Behavioral Science, Tulane University School of Medicine, New Orleans, LA, USA
| | - Qiaofeng Ye
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA
| | - Idan Shalev
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, PA, USA.
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9
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McGivern BB, Cronin DR, Ellenbogen JB, Borton MA, Knutson EL, Freire-Zapata V, Bouranis JA, Bernhardt L, Hernandez AI, Flynn RM, Woyda R, Cory AB, Wilson RM, Chanton JP, Woodcroft BJ, Ernakovich JG, Tfaily MM, Sullivan MB, Tyson GW, Rich VI, Hagerman AE, Wrighton KC. Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle. Nat Microbiol 2024; 9:1454-1466. [PMID: 38806673 PMCID: PMC11153144 DOI: 10.1038/s41564-024-01691-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/02/2024] [Indexed: 05/30/2024]
Abstract
With rising global temperatures, permafrost carbon stores are vulnerable to microbial degradation. The enzyme latch theory states that polyphenols should accumulate in saturated peatlands due to diminished phenol oxidase activity, inhibiting resident microbes and promoting carbon stabilization. Pairing microbiome and geochemical measurements along a permafrost thaw-induced saturation gradient in Stordalen Mire, a model Arctic peatland, we confirmed a negative relationship between phenol oxidase expression and saturation but failed to support other trends predicted by the enzyme latch. To inventory alternative polyphenol removal strategies, we built CAMPER, a gene annotation tool leveraging polyphenol enzyme knowledge gleaned across microbial ecosystems. Applying CAMPER to genome-resolved metatranscriptomes, we identified genes for diverse polyphenol-active enzymes expressed by various microbial lineages under a range of redox conditions. This shifts the paradigm that polyphenols stabilize carbon in saturated soils and highlights the need to consider both oxic and anoxic polyphenol metabolisms to understand carbon cycling in changing ecosystems.
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Affiliation(s)
- Bridget B McGivern
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, USA
| | - Dylan R Cronin
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Jared B Ellenbogen
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, USA
| | - Mikayla A Borton
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, USA
| | - Eleanor L Knutson
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA
| | | | - John A Bouranis
- Department of Environmental Science; University of Arizona, Tucson, AZ, USA
| | - Lukas Bernhardt
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| | - Alma I Hernandez
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| | - Rory M Flynn
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, USA
| | - Reed Woyda
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, USA
| | - Alexandra B Cory
- Department of Environmental Sciences, Emory University, Atlanta, GA, USA
| | - Rachel M Wilson
- Department of Earth Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, USA
| | - Jeffrey P Chanton
- Department of Earth Ocean and Atmospheric Sciences, Florida State University, Tallahassee, FL, USA
| | - Ben J Woodcroft
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Jessica G Ernakovich
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, USA
| | - Malak M Tfaily
- Department of Environmental Science; University of Arizona, Tucson, AZ, USA
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
- Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Gene W Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Virginia I Rich
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Ann E Hagerman
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, USA
| | - Kelly C Wrighton
- Department of Soil and Crop Science, Colorado State University, Fort Collins, CO, USA.
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10
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Chen L, Ma J, Xu W, Shen F, Yang Z, Sonne C, Dietz R, Li L, Jie X, Li L, Yan G, Zhang X. Comparative transcriptome and methylome of polar bears, giant and red pandas reveal diet-driven adaptive evolution. Evol Appl 2024; 17:e13731. [PMID: 38894980 PMCID: PMC11183199 DOI: 10.1111/eva.13731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 05/18/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
Abstract
Epigenetic regulation plays an important role in the evolution of species adaptations, yet little information is available on the epigenetic mechanisms underlying the adaptive evolution of bamboo-eating in both giant pandas (Ailuropoda melanoleuca) and red pandas (Ailurus fulgens). To investigate the potential contribution of epigenetic to the adaptive evolution of bamboo-eating in giant and red pandas, we performed hepatic comparative transcriptome and methylome analyses between bamboo-eating pandas and carnivorous polar bears (Ursus maritimus). We found that genes involved in carbohydrate, lipid, amino acid, and protein metabolism showed significant differences in methylation and expression levels between the two panda species and polar bears. Clustering analysis of gene expression revealed that giant pandas did not form a sister group with the more closely related polar bears, suggesting that the expression pattern of genes in livers of giant pandas and red pandas have evolved convergently driven by their similar diets. Compared to polar bears, some key genes involved in carbohydrate metabolism and biological oxidation and cholesterol synthesis showed hypomethylation and higher expression in giant and red pandas, while genes involved in fat digestion and absorption, fatty acid metabolism, lysine degradation, resistance to lipid peroxidation and detoxification showed hypermethylation and low expression. Our study elucidates the special nutrient utilization mechanism of giant pandas and red pandas and provides some insights into the molecular mechanism of their adaptive evolution of bamboo feeding. This has important implications for the breeding and conservation of giant pandas and red pandas.
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Affiliation(s)
- Lei Chen
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Jinnan Ma
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
- College of Continuing EducationYunnan Normal UniversityKunmingChina
| | - Wencai Xu
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Fujun Shen
- Sichuan Key Laboratory for Conservation Biology of Endangered WildlifeChengdu Research Base of Giant Panda BreedingChengduChina
| | | | - Christian Sonne
- Arctic Research Centre, Faculty of Science and Technology, Department of EcoscienceAarhus UniversityRoskildeDenmark
| | - Rune Dietz
- Arctic Research Centre, Faculty of Science and Technology, Department of EcoscienceAarhus UniversityRoskildeDenmark
| | - Linzhu Li
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Xiaodie Jie
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Lu Li
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Guoqiang Yan
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Xiuyue Zhang
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life SciencesSichuan UniversityChengduChina
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11
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Sagini MN, Zepp M, Eyol E, Ali DM, Gromova S, Dahlmann M, Behrens D, Groeschel C, Tischmeier L, Hoffmann J, Berger MR, Forssmann WG. EPI-X4, a CXCR4 antagonist inhibits tumor growth in pancreatic cancer and lymphoma models. Peptides 2024; 175:171111. [PMID: 38036098 DOI: 10.1016/j.peptides.2023.171111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 12/02/2023]
Abstract
Endogenous peptide inhibitor for CXCR4 (EPI-X4) is a CXCR4 antagonist with potential for cancer therapy. It is a processed fragment of serum albumin from the hemofiltrate of dialysis patients. This study reports the efficacy of fifteen EPI-X4 derivatives in pancreatic cancer and lymphoma models. In vitro, the peptides were investigated for antiproliferation (cytotoxicity) by MTT assay. The mRNA expression for CXCR4 and CXCL12 was determined by RT-PCR, chip array and RNA sequencing. Chip array analysis yielded 634 genes associated with CXCR4/CXCL12 signaling. About 21% of these genes correlated with metastasis in the context of cell motility, proliferation, and survival. Expression levels of these genes were altered in pancreatic cancer (36%), lymphoma models (53%) and in patients' data (58%). EPI-X4 derivatives failed to inhibit cell proliferation due to low expression of CXCR4 in vitro, but inhibited tumor growth in the bioassays with significant efficacy. In the pancreatic cancer model, EPI-X4a, f and k inhibited mean tumor growth by > 50% and even caused complete remissions. In the lymphoma model, EPI-X4b, n and p inhibited mean tumor growth by > 70% and caused stable disease. Given the non-toxic and non-immunogenic properties of EPI-X4, these findings underscore its status as a promising therapy of pancreatic cancer and lymphoma and warrant further studies. SIMPLE SUMMARY: This study examined the value of chemokine receptor CXCR4 as an antineoplastic target for the endogenous peptide inhibitor of CXCR4 (EPI-X4), a 12-meric peptide derived from serum albumin. EPI-X4 inhibits CXCR4 interaction with its natural ligand, CXCL12 (SDF1). Therefore, malignancies (including pancreatic cancer and lymphoma) that depend on the CXCR4/CXCL12 pathway for progression can be targeted with EPI-X4. Of 634 genes that were linked to the CXCR4/CXCL12 pathway, 21% were associated with metastasis. In cultured human Suit2-007 pancreatic cancer cells, CXCR4 showed low to undetectable expression, which was why EPI-X4 did not inhibit pancreatic cancer cell proliferation. These findings were different in vivo, where CXCR4 was highly expressed and EPI-X4 inhibited tumor growth in rodents harboring pancreatic cancer or lymphoma. In the pancreatic cancer model, EPI-X4 derivatives a, f and k caused complete remissions, while in lymphomas EPI-X4 derivatives b, n and p caused stable disease.
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Affiliation(s)
- Micah N Sagini
- Toxicology and Chemotherapy Unit, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Michael Zepp
- Toxicology and Chemotherapy Unit, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Ergül Eyol
- Toxicology and Chemotherapy Unit, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Doaa M Ali
- Toxicology and Chemotherapy Unit, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Svetlana Gromova
- EPO, Experimental Pharmacology & Oncology Berlin-Buch GmbH, Germany
| | - Mathias Dahlmann
- EPO, Experimental Pharmacology & Oncology Berlin-Buch GmbH, Germany
| | - Diana Behrens
- EPO, Experimental Pharmacology & Oncology Berlin-Buch GmbH, Germany
| | - Christian Groeschel
- NeoPep Pharma GmbH & Co. KG., Hannover, Germany and Hannover Medical School, Department of Internal Medicine, Germany
| | - Linus Tischmeier
- NeoPep Pharma GmbH & Co. KG., Hannover, Germany and Hannover Medical School, Department of Internal Medicine, Germany
| | - Jens Hoffmann
- EPO, Experimental Pharmacology & Oncology Berlin-Buch GmbH, Germany
| | - Martin R Berger
- Toxicology and Chemotherapy Unit, German Cancer Research Centre (DKFZ), Heidelberg, Germany.
| | - Wolf-Georg Forssmann
- NeoPep Pharma GmbH & Co. KG., Hannover, Germany and Hannover Medical School, Department of Internal Medicine, Germany.
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12
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Chereda H, Leha A, Beißbarth T. Stable feature selection utilizing Graph Convolutional Neural Network and Layer-wise Relevance Propagation for biomarker discovery in breast cancer. Artif Intell Med 2024; 151:102840. [PMID: 38658129 DOI: 10.1016/j.artmed.2024.102840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 03/05/2024] [Accepted: 03/10/2024] [Indexed: 04/26/2024]
Abstract
High-throughput technologies are becoming increasingly important in discovering prognostic biomarkers and in identifying novel drug targets. With Mammaprint, Oncotype DX, and many other prognostic molecular signatures breast cancer is one of the paradigmatic examples of the utility of high-throughput data to deliver prognostic biomarkers, that can be represented in a form of a rather short gene list. Such gene lists can be obtained as a set of features (genes) that are important for the decisions of a Machine Learning (ML) method applied to high-dimensional gene expression data. Several studies have identified predictive gene lists for patient prognosis in breast cancer, but these lists are unstable and have only a few genes in common. Instability of feature selection impedes biological interpretability: genes that are relevant for cancer pathology should be members of any predictive gene list obtained for the same clinical type of patients. Stability and interpretability of selected features can be improved by including information on molecular networks in ML methods. Graph Convolutional Neural Network (GCNN) is a contemporary deep learning approach applicable to gene expression data structured by a prior knowledge molecular network. Layer-wise Relevance Propagation (LRP) and SHapley Additive exPlanations (SHAP) are methods to explain individual decisions of deep learning models. We used both GCNN+LRP and GCNN+SHAP techniques to construct feature sets by aggregating individual explanations. We suggest a methodology to systematically and quantitatively analyze the stability, the impact on the classification performance, and the interpretability of the selected feature sets. We used this methodology to compare GCNN+LRP to GCNN+SHAP and to more classical ML-based feature selection approaches. Utilizing a large breast cancer gene expression dataset we show that, while feature selection with SHAP is useful in applications where selected features have to be impactful for classification performance, among all studied methods GCNN+LRP delivers the most stable (reproducible) and interpretable gene lists.
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Affiliation(s)
- Hryhorii Chereda
- Medical Bioinformatics, University Medical Center Göttingen, Goldschmidtstraße 1, Göttingen, 37077, Germany
| | - Andreas Leha
- Medical Bioinformatics, University Medical Center Göttingen, Goldschmidtstraße 1, Göttingen, 37077, Germany; Medical Statistics, University Medical Center Göttingen, Humboldtallee 32, Göttingen, 37073, Germany; Scientific Core Facility Medical Biometry and Statistical Bioinformatics, University Medical Center Göttingen, Humboldtallee 32, Göttingen, 37073, Germany
| | - Tim Beißbarth
- Medical Bioinformatics, University Medical Center Göttingen, Goldschmidtstraße 1, Göttingen, 37077, Germany; Campus-Institute Data Science (CIDAS), University of Göttingen, Goldschmidtstraße 1, Göttingen, 37077, Germany.
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13
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Leahy C, Osborne N, Shirota L, Rote P, Lee YK, Song BJ, Yin L, Zhang Y, Garcia V, Hardwick JP. The fatty acid omega hydroxylase genes (CYP4 family) in the progression of metabolic dysfunction-associated steatotic liver disease (MASLD): An RNA sequence database analysis and review. Biochem Pharmacol 2024:116241. [PMID: 38697309 DOI: 10.1016/j.bcp.2024.116241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/21/2024] [Accepted: 04/25/2024] [Indexed: 05/04/2024]
Abstract
Fatty acid omega hydroxylase P450s consist of enzymes that hydroxylate various chain-length saturated and unsaturated fatty acids (FAs) and bioactive eicosanoid lipids. The human cytochrome P450 gene 4 family (CYP4) consists of 12 members that are associated with several human diseases. However, their role in the progression of metabolic dysfunction-associated fatty liver disease (MASLD) remains largely unknown. It has long been thought that the induction of CYP4 family P450 during fasting and starvation prevents FA-related lipotoxicity through FA metabolism to dicarboxylic acids that are chain-shortened in peroxisomes and then transported to the mitochondria for complete oxidation. Several studies have revealed that peroxisome succinate transported to the mitochondria is used for gluconeogenesis during fasting and starvation, and recent evidence suggests that peroxisome acetate can be utilized for lipogenesis and lipid droplet formation as well as epigenetic modification of gene transcription. In addition, omega hydroxylation of the bioactive eicosanoid arachidonic acid to 20-Hydroxyeicosatetraenoic acid (20-HETE) is essential for activating the GPR75 receptor, leading to vasoconstriction and cell proliferation. Several mouse models of diet-induced MASLD have revealed the induction of selective CYP4A members and the suppression of CYP4F during steatosis and steatohepatitis, suggesting a critical metabolic role in the progression of fatty liver disease. Thus, to further investigate the functional roles of CYP4 genes, we analyzed the differential gene expression of 12 members of CYP4 gene family in datasets from the Gene Expression Omnibus (GEO) from patients with steatosis, steatohepatitis, fibrosis, cirrhosis, and hepatocellular carcinoma. We also observed the differential expression of various CYP4 genes in the progression of MASLD, indicating that different CYP4 members may have unique functional roles in the metabolism of specific FAs and eicosanoids at various stages of fatty liver disease. These results suggest that targeting selective members of the CYP4A family is a viable therapeutic approach for treating and managing MASLD.
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Affiliation(s)
- Charles Leahy
- Department of Integrative Medical Sciences Liver focus group, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH 44272, USA
| | - Nicholas Osborne
- Department of Integrative Medical Sciences Liver focus group, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH 44272, USA
| | - Leticia Shirota
- Department of Integrative Medical Sciences Liver focus group, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH 44272, USA
| | - Paula Rote
- Department of Integrative Medical Sciences Liver focus group, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH 44272, USA
| | - Yoon-Kwang Lee
- Department of Integrative Medical Sciences Liver focus group, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH 44272, USA
| | - Byoung-Joon Song
- Section of Molecular Pharmacology and Toxicology, National Institute on Alcohol Abuse and Alcoholism, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Liya Yin
- Department of Integrative Medical Sciences Liver focus group, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH 44272, USA
| | - Yanqiao Zhang
- Department of Integrative Medical Sciences Liver focus group, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH 44272, USA
| | - Victor Garcia
- Department of Pharmacology, New York Medical College, 15 Dana Road Science Building, Rm. 530, Valhalla, NY 10595, USA
| | - James P Hardwick
- Department of Integrative Medical Sciences Liver focus group, Northeast Ohio Medical University, 4209 State Route 44, Rootstown, OH 44272, USA.
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14
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Shen N, Xie H, Liu K, Li X, Wang L, Deng Y, Chen L, Bian Y, Xiao Y. Near-gapless genome and transcriptome analyses provide insights into fruiting body development in Lentinula edodes. Int J Biol Macromol 2024; 263:130610. [PMID: 38447851 DOI: 10.1016/j.ijbiomac.2024.130610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/01/2024] [Accepted: 03/02/2024] [Indexed: 03/08/2024]
Abstract
Fruiting body development in macrofungi is an intensive research subject. In this study, high-quality genomes were assembled for two sexually compatible monokaryons from a heterokaryotic Lentinula edodes strain WX1, and variations in L. edodes genomes were analyzed. Specifically, differential gene expression and allele-specific expression (ASE) were analyzed using the two monokaryotic genomes and transcriptome data from four different stages of fruiting body development in WX1. Results revealed that after aeration, mycelia sensed cell wall stress, pheromones, and a decrease in CO2 concentration, leading to up-regulated expression in genes related to cell adhesion, cell wall remodeling, proteolysis, and lipid metabolism, which may promote primordium differentiation. Aquaporin genes and those related to proteolysis, mitosis, lipid, and carbohydrate metabolism may play important roles in primordium development, while genes related to tissue differentiation and sexual reproduction were active in fruiting body. Several essential genes for fruiting body development were allele-specifically expressed and the two nuclear types could synergistically regulate fruiting body development by dominantly expressing genes with different functions. ASE was probably induced by long terminal repeat-retrotransposons. Findings here contribute to the further understanding of the mechanism of fruiting body development in macrofungi.
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Affiliation(s)
- Nan Shen
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Haoyu Xie
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Kefang Liu
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xinru Li
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Lu Wang
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Youjin Deng
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Lianfu Chen
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yinbing Bian
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yang Xiao
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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15
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Mohapatra G, Dachet F, Coleman LJ, Gillis B, Behm FG. Identification of unique genomic signatures in patients with fibromyalgia and chronic pain. Sci Rep 2024; 14:3949. [PMID: 38366049 PMCID: PMC10873305 DOI: 10.1038/s41598-024-53874-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
Fibromyalgia (FM) is a chronic pain syndrome characterized by widespread pain. The pathophysiology of fibromyalgia is not clearly understood and there are no specific biomarkers available for accurate diagnosis. Here we define genomic signatures using high throughput RNA sequencing on 96 fibromyalgia and 93 control cases. Our findings revealed three major fibromyalgia-associated expression signatures. The first group included 43 patients with a signature enriched for gene expression associated with extracellular matrix and downregulation of RhoGDI signaling pathway. The second group included 30 patients and showed a profound reduction in the expression of inflammatory mediators with an increased expression of genes involved in the CLEAR signaling pathway. These results suggest defective tissue homeostasis associated with the extra-cellular matrix and cellular program that regulates lysosomal biogenesis and participates in macromolecule clearance in fibromyalgia. The third group of 17 FM patients showed overexpression of pathways that control acute inflammation and dysfunction of the global transcriptional process. The result of this study indicates that FM is a heterogeneous and complex disease. Further elucidation of these pathways will lead to the development of accurate diagnostic markers, and effective therapeutic options for fibromyalgia.
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Affiliation(s)
- Gayatry Mohapatra
- Laboratory of Genomic Medicine, Department of Pathology, University of Illinois at Chicago (UIC) College of Medicine, 840 S. Wood St., Chicago, IL, 60612, USA.
| | - Fabien Dachet
- Laboratory of Genomic Medicine, Department of Pathology, University of Illinois at Chicago (UIC) College of Medicine, 840 S. Wood St., Chicago, IL, 60612, USA
| | - Louis J Coleman
- Laboratory of Genomic Medicine, Department of Pathology, University of Illinois at Chicago (UIC) College of Medicine, 840 S. Wood St., Chicago, IL, 60612, USA
| | - Bruce Gillis
- Department of Medicine, University of Illinois at Chicago (UIC) College of Medicine, Chicago, USA
| | - Frederick G Behm
- Laboratory of Genomic Medicine, Department of Pathology, University of Illinois at Chicago (UIC) College of Medicine, 840 S. Wood St., Chicago, IL, 60612, USA
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16
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Darragh K, Ramírez SR. The transcriptomic signature of adaptations associated with perfume collection in orchid bees. J Evol Biol 2024; 37:141-151. [PMID: 38271116 DOI: 10.1093/jeb/voad012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/11/2023] [Accepted: 11/23/2023] [Indexed: 01/27/2024]
Abstract
Secondary sexual traits can convey information on mate quality with the signal honesty maintained by the costly nature of trait expression. Mating signals are also often underpinned by physiological, morphological, and behavioural adaptations, which may require the evolution of novelty, but the genetic basis in many cases is unknown. In orchid bees, males acquire chemical compounds from the environment that act as pheromone-like bouquets (perfumes) during courtship displays. This process could be costly, potentially due to the cognitive demands of learning and the physiological demands of collecting a mix of extrinsic chemical compounds that may require detoxification. Furthermore, a novel trait, a specialized perfume pouch in the hind leg, is required for compound storage. We studied gene expression in the brain, hind leg, and Malpighian tubules-a tissue involved in detoxification-to investigate changes in gene expression following perfume collection. We detected upregulation of genes enriched in functions related to transcription, odorant binding, and receptor activity in the Malpighian tubules. On the other hand, we did not find any evidence for learning processes following perfume collection, or gene expression changes in the hind leg, perhaps due to constitutive expression, or the age of the sampled bees. We did identify high expression of chemosensory proteins in the hind legs, which we suggest could play a role in perfume collection or storage, with further functional studies necessary to determine their binding properties and potential physiological importance. Los rasgos sexuales secundarios pueden servir como indicadores de calidad de la pareja, y en algunos casos la honestidad de la señal se mantiene por el costo de expresar el rasgo. A menudo las señales sexuales están respaldadas por adaptaciones fisiológicas, morfológicas y de comportamiento por lo tanto pueden requerir la evolución de nuevos rasgos, pero en muchos casos se desconoce la base genética. En las abejas de las orquídeas, los machos recolectan compuestos químicos del medio ambiente, los cuales actúan como feromonas (perfumes) durante el despliegue de cortejo. Este proceso podría ser costoso, posiblemente debido a las demandas cognitivas del aprendizaje y las demandas fisiológicas de recolectar una mezcla de compuestos químicos extrínsecos que pueden requerir desintoxicación. Además, se requiere la evolución de un contenedor para almacenar perfumes en la pata trasera. Para investigar los cambios en la expresión génica después de la recolección de perfume, estudiamos la expresión génica en el cerebro, la pata trasera y los túbulos de Malpighi (tejido involucrado en la desintoxicación). Encontramos varios genes regulados positivamente en los túbulos de Malpighi después de la recolección que están enriquecidos en factores de transcripción, proteínas de fijación de olores, y proteínas con actividad de receptor. Por otro lado, no encontramos ninguna evidencia de procesos de aprendizaje posteriores a la recolección de perfumes, o cambios en la expresión génica en la pata trasera, esto quizás debido a la expresión constitutiva o la edad de las abejas muestreadas. Además, identificamos una alta expresión de proteínas quimio-sensoriales en las patas traseras, que podría desempeñar un papel en la recolección o almacenamiento de perfumes. Más estudios funcionales son necesarios para determinar las propiedades de fijación de las proteínas y su potencial importancia fisiológica.
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Affiliation(s)
- Kathy Darragh
- Department of Evolution and Ecology, University of California, Davis, CA, United States
| | - Santiago R Ramírez
- Department of Evolution and Ecology, University of California, Davis, CA, United States
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17
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Ellenbogen JB, Borton MA, McGivern BB, Cronin DR, Hoyt DW, Freire-Zapata V, McCalley CK, Varner RK, Crill PM, Wehr RA, Chanton JP, Woodcroft BJ, Tfaily MM, Tyson GW, Rich VI, Wrighton KC. Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost. mSystems 2024; 9:e0069823. [PMID: 38063415 PMCID: PMC10805028 DOI: 10.1128/msystems.00698-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/24/2023] [Indexed: 01/24/2024] Open
Abstract
While wetlands are major sources of biogenic methane (CH4), our understanding of resident microbial metabolism is incomplete, which compromises the prediction of CH4 emissions under ongoing climate change. Here, we employed genome-resolved multi-omics to expand our understanding of methanogenesis in the thawing permafrost peatland of Stordalen Mire in Arctic Sweden. In quadrupling the genomic representation of the site's methanogens and examining their encoded metabolism, we revealed that nearly 20% of the metagenome-assembled genomes (MAGs) encoded the potential for methylotrophic methanogenesis. Further, 27% of the transcriptionally active methanogens expressed methylotrophic genes; for Methanosarcinales and Methanobacteriales MAGs, these data indicated the use of methylated oxygen compounds (e.g., methanol), while for Methanomassiliicoccales, they primarily implicated methyl sulfides and methylamines. In addition to methanogenic methylotrophy, >1,700 bacterial MAGs across 19 phyla encoded anaerobic methylotrophic potential, with expression across 12 phyla. Metabolomic analyses revealed the presence of diverse methylated compounds in the Mire, including some known methylotrophic substrates. Active methylotrophy was observed across all stages of a permafrost thaw gradient in Stordalen, with the most frozen non-methanogenic palsa found to host bacterial methylotrophy and the partially thawed bog and fully thawed fen seen to house both methanogenic and bacterial methylotrophic activities. Methanogenesis across increasing permafrost thaw is thus revised from the sole dominance of hydrogenotrophic production and the appearance of acetoclastic at full thaw to consider the co-occurrence of methylotrophy throughout. Collectively, these findings indicate that methanogenic and bacterial methylotrophy may be an important and previously underappreciated component of carbon cycling and emissions in these rapidly changing wetland habitats.IMPORTANCEWetlands are the biggest natural source of atmospheric methane (CH4) emissions, yet we have an incomplete understanding of the suite of microbial metabolism that results in CH4 formation. Specifically, methanogenesis from methylated compounds is excluded from all ecosystem models used to predict wetland contributions to the global CH4 budget. Though recent studies have shown methylotrophic methanogenesis to be active across wetlands, the broad climatic importance of the metabolism remains critically understudied. Further, some methylotrophic bacteria are known to produce methanogenic by-products like acetate, increasing the complexity of the microbial methylotrophic metabolic network. Prior studies of Stordalen Mire have suggested that methylotrophic methanogenesis is irrelevant in situ and have not emphasized the bacterial capacity for metabolism, both of which we countered in this study. The importance of our findings lies in the significant advancement toward unraveling the broader impact of methylotrophs in wetland methanogenesis and, consequently, their contribution to the terrestrial global carbon cycle.
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Affiliation(s)
- Jared B. Ellenbogen
- Department of Soil and Crop Science, Colorado State University, Fort Collins, Colorado, USA
| | - Mikayla A. Borton
- Department of Soil and Crop Science, Colorado State University, Fort Collins, Colorado, USA
| | - Bridget B. McGivern
- Department of Soil and Crop Science, Colorado State University, Fort Collins, Colorado, USA
| | - Dylan R. Cronin
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - David W. Hoyt
- Environmental Molecular Sciences Laboratory, Earth and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | - Carmody K. McCalley
- Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA
| | - Ruth K. Varner
- Department of Earth Sciences and Institute for the Study of Earth, Oceans and Space, University of New Hampshire, Durham, New Hampshire, USA
| | - Patrick M. Crill
- Department of Geological Sciences, Bolin Center for Climate Research, Stockholm University, Stockholm, Sweden
| | - Richard A. Wehr
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Jeffrey P. Chanton
- Earth Ocean and Atmospheric Sciences, Florida State University, Tallahassee, Florida, USA
| | - Ben J. Woodcroft
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Malak M. Tfaily
- Department of Environmental Science, University of Arizona, Tucson, Arizona, USA
| | - Gene W. Tyson
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Virginia I. Rich
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Kelly C. Wrighton
- Department of Soil and Crop Science, Colorado State University, Fort Collins, Colorado, USA
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18
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Leleiwi I, Kokkinias K, Kim Y, Baniasad M, Shaffer M, Sabag-Daigle A, Daly RA, Flynn RM, Wysocki VH, Ahmer BMM, Borton MA, Wrighton KC. Gut microbiome carbon and sulfur metabolisms support Salmonella during pathogen infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575907. [PMID: 38293109 PMCID: PMC10827160 DOI: 10.1101/2024.01.16.575907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Salmonella enterica serovar Typhimurium is a pervasive enteric pathogen and an ongoing global threat to public health. Ecological studies in the Salmonella impacted gut remain underrepresented in the literature, discounting the microbiome mediated interactions that may inform Salmonella physiology during colonization and infection. To understand the microbial ecology of Salmonella remodeling of the gut microbiome, here we performed multi-omics approaches on fecal microbial communities from untreated and Salmonella -infected mice. Reconstructed genomes recruited metatranscriptomic and metabolomic data providing a strain-resolved view of the expressed metabolisms of the microbiome during Salmonella infection. This data informed possible Salmonella interactions with members of the gut microbiome that were previously uncharacterized. Salmonella- induced inflammation significantly reduced the diversity of transcriptionally active members in the gut microbiome, yet increased gene expression was detected for 7 members, with Luxibacter and Ligilactobacillus being the most active. Metatranscriptomic insights from Salmonella and other persistent taxa in the inflamed microbiome further expounded the necessity for oxidative tolerance mechanisms to endure the host inflammatory responses to infection. In the inflamed gut lactate was a key metabolite, with microbiota production and consumption reported amongst transcriptionally active members. We also showed that organic sulfur sources could be converted by gut microbiota to yield inorganic sulfur pools that become oxidized in the inflamed gut, resulting in thiosulfate and tetrathionate that supports Salmonella respiration. Advancement of pathobiome understanding beyond inferences from prior amplicon-based approaches can hold promise for infection mitigation, with the active community outlined here offering intriguing organismal and metabolic therapeutic targets.
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19
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Gersch S, Lange T, Beuthner BE, Elkenani M, Paul N, Schnelle M, Zeisberg E, Puls M, Hasenfuß G, Schuster A, Toischer K. Low-flow in aortic valve stenosis patients with reduced ejection fraction does not depend on left ventricular function. Clin Res Cardiol 2024:10.1007/s00392-023-02372-4. [PMID: 38236417 DOI: 10.1007/s00392-023-02372-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 12/30/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND Patients with severe aortic stenosis (AS) and reduced left ventricular ejection fraction (LVEF) can be distinguished into high- (HG) and low-gradient (LG) subgroups. However, less is known about their characteristics and underlying (pathophysiological) hemodynamic mechanisms. METHODS 98 AS patients with reduced LVEF were included. Subgroup characteristics were analyzed by a multimodal approach using clinical and histological data, next-generation sequencing (NGS) and applying echocardiography as well as cardiovascular magnetic resonance (CMR) imaging. Biopsy samples were analyzed with respect to fibrosis and mRNA expression profiles. RESULTS 40 patients were classified as HG-AS and 58 patients as LG-AS. Severity of AS was comparable between the subgroups. Comparison of both subgroups revealed no differences in LVEF (p = 0.1), LV mass (p = 0.6) or end-diastolic LV diameter (p = 0.12). Neither histological (HG: 23.2% vs. LG: 25.6%, p = 0.73) and circulating biomarker-based assessment (HG: 2.6 ± 2.2% vs. LG: 3.2 ± 3.1%; p = 0.46) of myocardial fibrosis nor global gene expression patterns differed between subgroups. Mitral regurgitation (MR), atrial fibrillation (AF) and impaired right ventricular function (MR: HG: 8% vs. LG: 24%; p < 0.001; AF: HG: 30% vs. LG: 51.7%; p = 0.03; RVSVi: HG 36.7 vs. LG 31.1 ml/m2, p = 0.045; TAPSE: HG 20.2 vs. LG 17.3 mm, p = 0.002) were more frequent in LG-AS patients compared to HG-AS. These pathologies could explain the higher mortality of LG vs. HG-AS patients. CONCLUSION In patients with low-flow severe aortic stenosis, low transaortic gradient and cardiac output are not primarily due to LV dysfunction or global changes in gene expression, but may be attributed to other additional cardiac pathologies like mitral regurgitation, atrial fibrillation or right ventricular dysfunction. These factors should also be considered during planning of aortic valve replacement.
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Affiliation(s)
- Svante Gersch
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Georg-August University, Robert-Koch-Straße 40, 37075, Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Göttingen, Germany
| | - Torben Lange
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Georg-August University, Robert-Koch-Straße 40, 37075, Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Göttingen, Germany
| | - Bo Eric Beuthner
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Georg-August University, Robert-Koch-Straße 40, 37075, Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Göttingen, Germany
| | - Manar Elkenani
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Georg-August University, Robert-Koch-Straße 40, 37075, Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Göttingen, Germany
| | - Niels Paul
- Department of Bioinformatics, University Medical Center Göttingen, Georg-August University, Göttingen, Germany
| | - Moritz Schnelle
- German Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Göttingen, Germany
- Department of Clinical Chemistry, University Medical Center Göttingen, Georg-August University, Göttingen, Germany
| | - Elisabeth Zeisberg
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Georg-August University, Robert-Koch-Straße 40, 37075, Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Göttingen, Germany
| | - Miriam Puls
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Georg-August University, Robert-Koch-Straße 40, 37075, Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Göttingen, Germany
| | - Gerd Hasenfuß
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Georg-August University, Robert-Koch-Straße 40, 37075, Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Göttingen, Germany
| | - Andreas Schuster
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Georg-August University, Robert-Koch-Straße 40, 37075, Göttingen, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Göttingen, Germany
| | - Karl Toischer
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Georg-August University, Robert-Koch-Straße 40, 37075, Göttingen, Germany.
- German Centre for Cardiovascular Research (DZHK), Partner Site Göttingen, Göttingen, Germany.
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20
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Lawrence BT, Calle A, Saski CA, Melgar JC. Differential Gene Expression Patterns in Peach Roots under Non-Uniform Soil Conditions in Response to Organic Matter. Genes (Basel) 2024; 15:70. [PMID: 38254960 PMCID: PMC10815151 DOI: 10.3390/genes15010070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/01/2023] [Accepted: 01/01/2024] [Indexed: 01/24/2024] Open
Abstract
Organic matter (OM) amendments are often encouraged in sustainable agriculture programs but can create heterogeneous soil environments when applied to perennial crops such as peaches (Prunus persica (L.) Batsch). To better understand the responses of peach roots to non-uniform soil conditions, transcriptomic analysis was performed in a split-root study using uniform soil (the same soil type for all roots) or non-uniform soil (different soil types for each half of the root system) from either (1) autoclaved sand (S), (2) autoclaved sand with autoclaved compost (A), or (3) autoclaved sand with compost which included inherent biological soil life (B). Each uniform soil type (S, A, and B) was grouped and compared by uniform and non-uniform soil comparisons for a total of nine treatments. Comparisons revealed peach roots had differentially expressed genes (DEGs) and gene ontology terms between soil groups, with the S and B groups having a range of 106-411 DEGs and the A group having a range of 19-94 DEGs. Additionally, six modules were identified and correlated (p > 0.69) for six of the nine treatment combinations. This study broadly highlights the complexity of how OM and biological life in the rhizosphere interact with immediate and distant roots and sheds light on how non-homogenous soil conditions can influence peach root gene expression.
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Affiliation(s)
- Brian T. Lawrence
- Department of Plant and Environmental Sciences, Clemson University, 105 Collings Street, Clemson, SC 29634, USA
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, NY 14456, USA
| | - Alejandro Calle
- Department of Plant and Environmental Sciences, Clemson University, 105 Collings Street, Clemson, SC 29634, USA
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Fruitcentre, PCiTAL, Gardeny Park, Fruitcentre Building, 25003 Lleida, Spain
| | - Christopher A. Saski
- Department of Plant and Environmental Sciences, Clemson University, 105 Collings Street, Clemson, SC 29634, USA
| | - Juan Carlos Melgar
- Department of Plant and Environmental Sciences, Clemson University, 105 Collings Street, Clemson, SC 29634, USA
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21
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Golconda P, Andrade-Medina M, Oberstein A. Subconfluent ARPE-19 Cells Display Mesenchymal Cell-State Characteristics and Behave like Fibroblasts, Rather Than Epithelial Cells, in Experimental HCMV Infection Studies. Viruses 2023; 16:49. [PMID: 38257749 PMCID: PMC10821009 DOI: 10.3390/v16010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Human cytomegalovirus (HCMV) has a broad cellular tropism and epithelial cells are important physiological targets during infection. The retinal pigment epithelial cell line ARPE-19 has been used to model HCMV infection in epithelial cells for decades and remains a commonly used cell type for studying viral entry, replication, and the cellular response to infection. We previously found that ARPE-19 cells, despite being derived from an epithelial cell explant, express extremely low levels of canonical epithelial proteins, such as E-cadherin and EpCAM. Here, we perform comparative studies of ARPE-19 and additional epithelial cell lines with strong epithelial characteristics. We find that ARPE-19 cells cultured under subconfluent conditions resemble mesenchymal fibroblasts, rather than epithelial cells; this is consistent with previous studies showing that ARPE-19 cultures require extended periods of high confluency culture to maintain epithelial characteristics. By reanalyzing public gene expression data and using machine learning, we find evidence that ARPE-19 cultures maintained across many labs exhibit mesenchymal characteristics and that the majority of studies employing ARPE-19 use them in a mesenchymal state. Lastly, by performing experimental HCMV infections across mesenchymal and epithelial cell lines, we find that ARPE-19 cells behave like mesenchymal fibroblasts, producing logarithmic yields of cell-free infectious progeny, while cell lines with strong epithelial character exhibit an atypical infectious cycle and naturally restrict the production of cell-free progeny. Our work highlights important characteristics of the ARPE-19 cell line and suggests that subconfluent ARPE-19 cells may not be optimal for modeling epithelial infection with HCMV or other human viruses. It also suggests that HCMV biosynthesis and/or spread may occur quite differently in epithelial cells compared to mesenchymal cells. These differences could contribute to viral persistence or pathogenesis in epithelial tissues.
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Affiliation(s)
| | | | - Adam Oberstein
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, 835 South Wolcott Ave., Chicago, IL 60612, USA; (P.G.); (M.A.-M.)
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22
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Gao H, Li Y, Tian Y, Zhang H, Kim K, Li B. Gene family expansion analysis and identification of the histone family in Spodoptera frugiperda. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 48:101142. [PMID: 37713926 DOI: 10.1016/j.cbd.2023.101142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/03/2023] [Accepted: 09/04/2023] [Indexed: 09/17/2023]
Abstract
Spodoptera frugiperda, a major invasive pest, causes severe damage to various economically important crops. Previous comparative genomics studies have revealed a close association between the invasiveness of S. frugiperda and its genome. In recent years, a vast amount of genome from lepidopteran species has become available, offering an opportunity for a more detailed and comprehensive understanding of the biological characteristics of S. frugiperda. In this study, we conducted a comprehensive comparative genomics analysis of S. frugiperda using genome from 46 lepidopteran species. We found the highest number of gene family expansion events in S. frugiperda, indicating that gene family expansion is a crucial mechanism in its adaptive evolution. The expanded gene families are enriched in various biological processes, including nutrient metabolism, development, stress response, reproduction, and immune processes, suggesting that the expansion of these gene families likely contributes to the strong environmental adaptability of S. frugiperda. Furthermore, we identified the expansion of histone gene families in S. frugiperda which resulted from chromosome segmental duplications after the divergence from closely related species. Expression analysis of histone genes indicated that certain members might exert an influence on the growth and reproduction processes of S. frugiperda. Overall, our study deepens our understanding of the biological characteristics of S. frugiperda, providing a theoretical basis for the comprehensive management and sustained control of S. frugiperda and other lepidopteran pests in the future.
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Affiliation(s)
- Han Gao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Yanxiao Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Ying Tian
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - Hui Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China
| | - KumChol Kim
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China; Department of Life-Science, University of Science, Pyongyang, Democratic People's Republic of Korea
| | - Bin Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China.
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23
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Verschoor N, Smid M, Jager A, Sleijfer S, Wilting SM, Martens JWM. Integrative whole-genome and transcriptome analysis of HER2-amplified metastatic breast cancer. Breast Cancer Res 2023; 25:145. [PMID: 37968696 PMCID: PMC10648326 DOI: 10.1186/s13058-023-01743-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/06/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND In breast cancer, the advent of anti-HER2 therapies has made HER2+ tumors a highly relevant subgroup. However, the exact characteristics which prohibit clinical response to anti-HER2 therapies and drive disease progression are not yet fully known. Integrative whole-genome and transcriptomic sequencing data from both primary and metastatic HER2-positive breast cancer will enhance our understanding of underlying biological processes. METHODS Here, we used WGS and RNA sequencing data of 700 metastatic breast tumors, of which 68 being HER2+, to search for specific genomic features of HER2+ disease and therapy resistance. Furthermore, we integrated results with transcriptomic data to associate tumors exhibiting a HER2+-specific gene expression profile with ERBB2 mutation status, prior therapy and relevant gene expression signatures. RESULTS Overall genomic profiles of primary and metastatic HER2+ breast cancers were similar, and no specific acquired genomics traits connected to prior anti-HER2 treatment were observed. However, specific genomic features were predictive of progression-free survival on post-biopsy anti-HER2 treatment. Furthermore, a HER2-driven expression profile grouped HER2-amplified tumors with ERBB2-mutated cases and cases without HER2 alterations. The latter were reported as ER positive in primary disease, but the metastatic biopsy showed low ESR1 expression and upregulation of the MAPK pathway, suggesting transformation to ER independence. CONCLUSIONS In summary, although the quantity of variants increased throughout HER2-positive breast cancer progression, the genomic composition remained largely consistent, thus yielding no new major processes beside those already operational in primary disease. Our results suggest that integrated genomic and transcriptomic analyses may be key in establishing therapeutic options.
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Affiliation(s)
- Noortje Verschoor
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - Saskia M Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands
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24
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Sukko N, Kalapanulak S, Saithong T. Trehalose metabolism coordinates transcriptional regulatory control and metabolic requirements to trigger the onset of cassava storage root initiation. Sci Rep 2023; 13:19973. [PMID: 37968317 PMCID: PMC10651926 DOI: 10.1038/s41598-023-47095-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023] Open
Abstract
Cassava storage roots (SR) are an important source of food energy and raw material for a wide range of applications. Understanding SR initiation and the associated regulation is critical to boosting tuber yield in cassava. Decades of transcriptome studies have identified key regulators relevant to SR formation, transcriptional regulation and sugar metabolism. However, there remain uncertainties over the roles of the regulators in modulating the onset of SR development owing to the limitation of the widely applied differential gene expression analysis. Here, we aimed to investigate the regulation underlying the transition from fibrous (FR) to SR based on Dynamic Network Biomarker (DNB) analysis. Gene expression analysis during cassava root initiation showed the transition period to SR happened in FR during 8 weeks after planting (FR8). Ninety-nine DNB genes associated with SR initiation and development were identified. Interestingly, the role of trehalose metabolism, especially trehalase1 (TRE1), in modulating metabolites abundance and coordinating regulatory signaling and carbon substrate availability via the connection of transcriptional regulation and sugar metabolism was highlighted. The results agree with the associated DNB characters of TRE1 reported in other transcriptome studies of cassava SR initiation and Attre1 loss of function in literature. The findings help fill the knowledge gap regarding the regulation underlying cassava SR initiation.
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Affiliation(s)
- Nattavat Sukko
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand
| | - Saowalak Kalapanulak
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand.
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand.
- Center for Agricultural Systems Biology, Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand.
| | - Treenut Saithong
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology and School of Information Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand.
- School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand.
- Center for Agricultural Systems Biology, Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (Bang Khun Thian), Bangkok, 10150, Thailand.
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25
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Borton MA, Shaffer M, Hoyt DW, Jiang R, Ellenbogen JB, Purvine S, Nicora CD, Eder EK, Wong AR, Smulian AG, Lipton MS, Krzycki JA, Wrighton KC. Targeted curation of the gut microbial gene content modulating human cardiovascular disease. mBio 2023; 14:e0151123. [PMID: 37695138 PMCID: PMC10653893 DOI: 10.1128/mbio.01511-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 09/12/2023] Open
Abstract
IMPORTANCE One of the most-cited examples of the gut microbiome modulating human disease is the microbial metabolism of quaternary amines from protein-rich foods. By-products of this microbial processing promote atherosclerotic heart disease, a leading cause of human mortality globally. Our research addresses current knowledge gaps in our understanding of this microbial metabolism by holistically inventorying the microorganisms and expressed genes catalyzing critical atherosclerosis-promoting and -ameliorating reactions in the human gut. This led to the creation of an open-access resource, the Methylated Amine Gene Inventory of Catabolism database, the first systematic inventory of gut methylated amine metabolism. More importantly, using this resource we deliver here, we show for the first time that these gut microbial genes can predict human disease, paving the way for microbiota-inspired diagnostics and interventions.
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Affiliation(s)
- Mikayla A. Borton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Michael Shaffer
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - David W. Hoyt
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Ruisheng Jiang
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | | | - Samuel Purvine
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Carrie D. Nicora
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Elizabeth K. Eder
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Allison R. Wong
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - A. George Smulian
- Department of Internal Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Mary S. Lipton
- Environmental and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Joseph A. Krzycki
- Department of Microbiology, The Ohio State University, Columbus, Ohio, USA
| | - Kelly C. Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA
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26
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Hoskins JW, Christensen TA, Amundadottir LT. Master regulator activity QTL protocol to implicate regulatory pathways potentially mediating GWAS signals using eQTL data. STAR Protoc 2023; 4:102362. [PMID: 37330907 PMCID: PMC10285694 DOI: 10.1016/j.xpro.2023.102362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 04/26/2023] [Accepted: 05/17/2023] [Indexed: 06/20/2023] Open
Abstract
Here, we present a protocol to identify transcriptional regulators potentially mediating downstream biological effects of germline variants associated with complex traits of interest, which enables functional hypothesis generation independent of colocalizing expression quantitative trait loci (eQTLs). We describe steps for tissue-/cell-type-specific co-expression network modeling, expression regulator activity inference, and identification of representative phenotypic master regulators. Finally, we detail activity QTL and eQTL analyses. This protocol requires genotype, expression, and relevant covariables and phenotype data from existing eQTL datasets. For complete details on the use and execution of this protocol, please refer to Hoskins et al.1.
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Affiliation(s)
- Jason W Hoskins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MA 20892, USA.
| | - Trevor A Christensen
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MA 20892, USA
| | - Laufey T Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MA 20892, USA.
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27
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Angus L, Smid M, Wilting SM, Bos MK, Steeghs N, Konings IRHM, Tjan-Heijnen VCG, van Riel JMGH, van de Wouw AJ, Cuppen E, Lolkema MP, Jager A, Sleijfer S, Martens JWM. Genomic Alterations Associated with Estrogen Receptor Pathway Activity in Metastatic Breast Cancer Have a Differential Impact on Downstream ER Signaling. Cancers (Basel) 2023; 15:4416. [PMID: 37686693 PMCID: PMC10487136 DOI: 10.3390/cancers15174416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023] Open
Abstract
Mutations in the estrogen receptor gene (ESR1), its transcriptional regulators, and the mitogen-activated protein kinase (MAPK) pathway are enriched in patients with endocrine-resistant metastatic breast cancer (MBC). Here, we integrated whole genome sequencing with RNA sequencing data from the same samples of 101 ER-positive/HER2-negative MBC patients who underwent a tumor biopsy prior to the start of a new line of treatment for MBC (CPCT-02 study, NCT01855477) to analyze the downstream effects of DNA alterations previously linked to endocrine resistance, thereby gaining a better understanding of the associated mechanisms. Hierarchical clustering was performed using expression of ESR1 target genes. Genomic alterations at the DNA level, gene expression levels, and last administered therapy were compared between the identified clusters. Hierarchical clustering revealed two distinct clusters, one of which was characterized by increased expression of ESR1 and its target genes. Samples in this cluster were significantly enriched for mutations in ESR1 and amplifications in FGFR1 and TSPYL. Patients in the other cluster showed relatively lower expression levels of ESR1 and its target genes, comparable to ER-negative samples, and more often received endocrine therapy as their last treatment before biopsy. Genes in the MAPK-pathway, including NF1, and ESR1 transcriptional regulators were evenly distributed. In conclusion, RNA sequencing identified a subgroup of patients with clear expression of ESR1 and its downstream targets, probably still benefiting from ER-targeting agents. The lower ER expression in the other subgroup might be partially explained by ER activity still being blocked by recently administered endocrine treatment, indicating that biopsy timing relative to endocrine treatment needs to be considered when interpreting transcriptomic data.
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Affiliation(s)
- Lindsay Angus
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Cancer, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (M.S.); (S.M.W.); (M.K.B.); (M.P.L.); (A.J.); (S.S.); (J.W.M.M.)
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Cancer, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (M.S.); (S.M.W.); (M.K.B.); (M.P.L.); (A.J.); (S.S.); (J.W.M.M.)
| | - Saskia M. Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Cancer, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (M.S.); (S.M.W.); (M.K.B.); (M.P.L.); (A.J.); (S.S.); (J.W.M.M.)
| | - Manouk K. Bos
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Cancer, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (M.S.); (S.M.W.); (M.K.B.); (M.P.L.); (A.J.); (S.S.); (J.W.M.M.)
| | - Neeltje Steeghs
- Department of Medical Oncology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
- Center for Personalized Cancer Treatment, 6500 HB Nijmegen, The Netherlands; (V.C.G.T.-H.)
| | - Inge R. H. M. Konings
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands;
| | - Vivianne C. G. Tjan-Heijnen
- Center for Personalized Cancer Treatment, 6500 HB Nijmegen, The Netherlands; (V.C.G.T.-H.)
- Department of Medical Oncology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, 6229 HX Maastricht, The Netherlands
| | | | - Agnes J. van de Wouw
- Department of Medical Oncology, VieCuri Medical Center, 5912 BL Venlo, The Netherlands;
| | - CPCT Consortium
- Center for Personalized Cancer Treatment, 6500 HB Nijmegen, The Netherlands; (V.C.G.T.-H.)
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands;
- Hartwig Medical Foundation, 1098 XH Amsterdam, The Netherlands
| | - Martijn P. Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Cancer, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (M.S.); (S.M.W.); (M.K.B.); (M.P.L.); (A.J.); (S.S.); (J.W.M.M.)
- Center for Personalized Cancer Treatment, 6500 HB Nijmegen, The Netherlands; (V.C.G.T.-H.)
| | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Cancer, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (M.S.); (S.M.W.); (M.K.B.); (M.P.L.); (A.J.); (S.S.); (J.W.M.M.)
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Cancer, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (M.S.); (S.M.W.); (M.K.B.); (M.P.L.); (A.J.); (S.S.); (J.W.M.M.)
- Center for Personalized Cancer Treatment, 6500 HB Nijmegen, The Netherlands; (V.C.G.T.-H.)
| | - John W. M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Cancer, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands; (M.S.); (S.M.W.); (M.K.B.); (M.P.L.); (A.J.); (S.S.); (J.W.M.M.)
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Brink DP, Mierke F, Norbeck J, Siewers V, Andlid T. Expanding the genetic toolbox of Rhodotorula toruloides by identification and validation of six novel promoters induced or repressed under nitrogen starvation. Microb Cell Fact 2023; 22:160. [PMID: 37598166 PMCID: PMC10440040 DOI: 10.1186/s12934-023-02175-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/09/2023] [Indexed: 08/21/2023] Open
Abstract
BACKGROUND The non-conventional yeast Rhodotorula toruloides is an emerging host organism in biotechnology by merit of its natural capacity to accumulate high levels of carotenoids and intracellular storage lipids from a variety of carbon sources. While the number of genetic engineering strategies that employ R. toruloides is increasing, the lack of genetic tools available for modification of this yeast is still limiting strain development. For instance, several strong, constitutive R. toruloides promoters have been characterized, but to date, only five inducible promoters have been identified. Although nitrogen-limited cultivation conditions are commonly used to induce lipid accumulation in this yeast, no promoters regulated by nitrogen starvation have been described for R. toruloides. RESULTS In this study, we used a combination of genomics and transcriptomics methods to identify novel R. toruloides promoter sequences that are either inducible or repressible by nitrogen starvation. RNA sequencing was used to assess gene expression in the recently isolated strain R. toruloides BOT-A2 during exponential growth and during nitrogen starvation, when cultivated with either glucose or xylose as the carbon source. The genome of BOT-A2 was sequenced using a combination of long- and short-read sequencing and annotated with support of the RNAseq data. Differential expression analysis was used to identify genes with a |log2 fold change|≥ 2 when comparing their expression during nitrogen depletion to that during exponential growth. The promoter regions from 16 of these genes were evaluated for their ability to drive the expression of a fluorescent reporter gene. Three promoters that were clearly upregulated under nitrogen starvation and three that were downregulated were selected and further characterized. One promoter, derived from gene RTBOTA2_003877, was found to function like an on-off switch, as it was only upregulated under full nitrogen depletion and downregulated in the presence of the nitrogen source. CONCLUSIONS Six new R. toruloides promoters that were either upregulated or downregulated under nitrogen-starvation were identified. These substantially contribute to the available promoters when engineering this organism and are foreseen to be particularly useful for future engineering strategies requiring specific regulation of target genes in accordance with nitrogen availability.
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Affiliation(s)
- Daniel P Brink
- Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Friederike Mierke
- Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Joakim Norbeck
- Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Verena Siewers
- Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden.
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
| | - Thomas Andlid
- Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
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29
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MacPherson RA, Shankar V, Anholt RRH, Mackay TFC. Genetic and genomic analyses of Drosophila melanogaster models of chromatin modification disorders. Genetics 2023; 224:iyad061. [PMID: 37036413 PMCID: PMC10411607 DOI: 10.1093/genetics/iyad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/10/2022] [Accepted: 03/30/2023] [Indexed: 04/11/2023] Open
Abstract
Switch/sucrose nonfermentable (SWI/SNF)-related intellectual disability disorders (SSRIDDs) and Cornelia de Lange syndrome are rare syndromic neurodevelopmental disorders with overlapping clinical phenotypes. SSRIDDs are associated with the BAF (Brahma-Related Gene-1 associated factor) complex, whereas CdLS is a disorder of chromatin modification associated with the cohesin complex. Here, we used RNA interference in Drosophila melanogaster to reduce the expression of six genes (brm, osa, Snr1, SMC1, SMC3, vtd) orthologous to human genes associated with SSRIDDs and CdLS. These fly models exhibit changes in sleep, activity, startle behavior (a proxy for sensorimotor integration), and brain morphology. Whole genome RNA sequencing identified 9,657 differentially expressed genes (FDR < 0.05), 156 of which are differentially expressed in both sexes in SSRIDD- and CdLS-specific analyses, including Bap60, which is orthologous to SMARCD1, an SSRIDD-associated BAF component. k-means clustering reveals genes co-regulated within and across SSRIDD and CdLS fly models. RNAi-mediated reduction of expression of six genes co-regulated with focal genes brm, osa, and/or Snr1 recapitulated changes in the behavior of the focal genes. Based on the assumption that fundamental biological processes are evolutionarily conserved, Drosophila models can be used to understand underlying molecular effects of variants in chromatin-modification pathways and may aid in the discovery of drugs that ameliorate deleterious phenotypic effects.
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Affiliation(s)
- Rebecca A MacPherson
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Vijay Shankar
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Robert R H Anholt
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Trudy F C Mackay
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
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Lázaro J, Costanzo M, Sanaki-Matsumiya M, Girardot C, Hayashi M, Hayashi K, Diecke S, Hildebrandt TB, Lazzari G, Wu J, Petkov S, Behr R, Trivedi V, Matsuda M, Ebisuya M. A stem cell zoo uncovers intracellular scaling of developmental tempo across mammals. Cell Stem Cell 2023; 30:938-949.e7. [PMID: 37343565 PMCID: PMC10321541 DOI: 10.1016/j.stem.2023.05.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 04/03/2023] [Accepted: 05/25/2023] [Indexed: 06/23/2023]
Abstract
Differential speeds in biochemical reactions have been proposed to be responsible for the differences in developmental tempo between mice and humans. However, the underlying mechanism controlling the species-specific kinetics remains to be determined. Using in vitro differentiation of pluripotent stem cells, we recapitulated the segmentation clocks of diverse mammalian species varying in body weight and taxa: marmoset, rabbit, cattle, and rhinoceros. Together with mouse and human, the segmentation clock periods of the six species did not scale with the animal body weight, but with the embryogenesis length. The biochemical kinetics of the core clock gene HES7 displayed clear scaling with the species-specific segmentation clock period. However, the cellular metabolic rates did not show an evident correlation. Instead, genes involving biochemical reactions showed an expression pattern that scales with the segmentation clock period. Altogether, our stem cell zoo uncovered general scaling laws governing species-specific developmental tempo.
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Affiliation(s)
- Jorge Lázaro
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Maria Costanzo
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Marina Sanaki-Matsumiya
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Charles Girardot
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Masafumi Hayashi
- Department of Genome Biology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Katsuhiko Hayashi
- Department of Genome Biology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Sebastian Diecke
- Technology Platform Pluripotent Stem Cells, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | | | | | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Stoyan Petkov
- Platform Degenerative Diseases, German Primate Center - Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany; German Center for Cardiovascular Research (DZHK), Partner site Göttingen, Göttingen, Germany
| | - Rüdiger Behr
- Platform Degenerative Diseases, German Primate Center - Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany; German Center for Cardiovascular Research (DZHK), Partner site Göttingen, Göttingen, Germany
| | - Vikas Trivedi
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain.
| | - Mitsuhiro Matsuda
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain.
| | - Miki Ebisuya
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain; Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany.
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Yizhen Z, Chen L, Jie X, Shen F, Zhang L, Hou Y, Li L, Yan G, Zhang X, Yang Z. Comparative study of the digestion and metabolism related genes' expression changes during the postnatal food change in different dietary mammals. Front Genet 2023; 14:1198977. [PMID: 37470038 PMCID: PMC10352678 DOI: 10.3389/fgene.2023.1198977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 06/26/2023] [Indexed: 07/21/2023] Open
Abstract
The changes in the expression of genes related to digestion and metabolism may be various in different dietary mammals from juvenile to adult, especially, the giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens), which were once carnivores but have shifted to being specialized bamboo eaters, are unique features of their changes are more unclear. To elucidate the changing patterns of gene expression related to digestion and metabolism from juvenile to adult in different dietary mammals, we performed transcriptome analysis of the liver or pancreas in giant and red pandas, herbivorous rabbits (Oryctolagus cuniculus) and macaques (Macaca mulatta), carnivorous ferrets (Mustela putorius furo), and omnivorous mice (Mus musculus) from juvenile to adult. During the transition from juvenile to adulthood, giant and red pandas, as well as rabbits and macaques, show significant upregulation of key genes for carbohydrate metabolism, such as starch hydrolysis and sucrose metabolism, and unsaturated fatty acid metabolism, such as linoleic acid, while there is no significant difference in the expression of key genes for fatty acid β-oxidation. A large number of amino acid metabolism related genes were upregulated in adult rabbits and macaques compared to juveniles. While adult giant and red pandas mainly showed upregulation of key genes for arginine synthesis and downregulation of key genes for arginine and lysine degradation. In adult stages, mouse had significantly higher expression patterns in key genes for starch hydrolysis and sucrose metabolism, as well as lipid and protein metabolism. In contrast to general expectations, genes related to lipid, amino acid and protein metabolism were significantly higher expressed in adult group of ferrets, which may be related to their high metabolic levels. Our study elucidates the pattern of changes in the expression of genes related to digestion and metabolism from juvenile to adult in different dietary mammals, with giant and red pandas showing adaptations associated with specific nutritional limitations of bamboo.
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Affiliation(s)
| | - Lei Chen
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiaodie Jie
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Fujun Shen
- Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Liang Zhang
- Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Yusen Hou
- Pharmacy College, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Lu Li
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Guoqiang Yan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiuyue Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
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Gao H, Li Y, Zhang H, Wang S, Feng F, Tang J, Li B. Comparative study of neuropeptide signaling systems in Hemiptera. INSECT SCIENCE 2023; 30:705-724. [PMID: 36165207 DOI: 10.1111/1744-7917.13120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/27/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
Numerous physiological processes in insects are tightly regulated by neuropeptides and their receptors. Although they form an ancient signaling system, there is still a great deal of variety in neuropeptides and their receptors among different species within the same order. Neuropeptides and their receptors have been documented in many hemipteran insects, but the differences among them have been poorly characterized. Commercial grapevines worldwide are plagued by the bug Daktulosphaira vitifoliae (Hemiptera: Sternorrhyncha). Here, 33 neuropeptide precursors and 48 putative neuropeptide G protein-coupled receptor (GPCR) genes were identified in D. vitifoliae. Their expression profiles at the probe and feeding stages reflected potential regulatory roles in probe behavior. By comparison, we found that the Releasing Hormone-Related Peptides (GnRHs) system of Sternorrhyncha was differentiated from those of the other 2 suborders in Hemiptera. Independent secondary losses of the adipokinetic hormone/corazonin-related peptide receptor (ACP) and corazonin (CRZ) occurred during the evolution of Sternorrhyncha. Additionally, we discovered that the neuropeptide signaling systems of Sternorrhyncha were very different from those of Heteroptera and Auchenorrhyncha, which was consistent with Sternorrhyncha's phylogenetic position at the base of the order. This research provides more knowledge on neuropeptide systems and sets the groundwork for the creation of novel D. vitifoliae management strategies that specifically target these signaling pathways.
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Affiliation(s)
- Han Gao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yanxiao Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Hui Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Suisui Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Fan Feng
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jing Tang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Bin Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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33
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Leleiwi I, Rodriguez-Ramos J, Shaffer M, Sabag-Daigle A, Kokkinias K, Flynn RM, Daly RA, Kop LFM, Solden LM, Ahmer BMM, Borton MA, Wrighton KC. Exposing new taxonomic variation with inflammation - a murine model-specific genome database for gut microbiome researchers. MICROBIOME 2023; 11:114. [PMID: 37210515 PMCID: PMC10199544 DOI: 10.1186/s40168-023-01529-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/21/2023] [Indexed: 05/22/2023]
Abstract
BACKGROUND The murine CBA/J mouse model widely supports immunology and enteric pathogen research. This model has illuminated Salmonella interactions with the gut microbiome since pathogen proliferation does not require disruptive pretreatment of the native microbiota, nor does it become systemic, thereby representing an analog to gastroenteritis disease progression in humans. Despite the value to broad research communities, microbiota in CBA/J mice are not represented in current murine microbiome genome catalogs. RESULTS Here we present the first microbial and viral genomic catalog of the CBA/J murine gut microbiome. Using fecal microbial communities from untreated and Salmonella-infected, highly inflamed mice, we performed genomic reconstruction to determine the impacts on gut microbiome membership and functional potential. From high depth whole community sequencing (~ 42.4 Gbps/sample), we reconstructed 2281 bacterial and 4516 viral draft genomes. Salmonella challenge significantly altered gut membership in CBA/J mice, revealing 30 genera and 98 species that were conditionally rare and unsampled in non-inflamed mice. Additionally, inflamed communities were depleted in microbial genes that modulate host anti-inflammatory pathways and enriched in genes for respiratory energy generation. Our findings suggest decreases in butyrate concentrations during Salmonella infection corresponded to reductions in the relative abundance in members of the Alistipes. Strain-level comparison of CBA/J microbial genomes to prominent murine gut microbiome databases identified newly sampled lineages in this resource, while comparisons to human gut microbiomes extended the host relevance of dominant CBA/J inflammation-resistant strains. CONCLUSIONS This CBA/J microbiome database provides the first genomic sampling of relevant, uncultivated microorganisms within the gut from this widely used laboratory model. Using this resource, we curated a functional, strain-resolved view on how Salmonella remodels intact murine gut communities, advancing pathobiome understanding beyond inferences from prior amplicon-based approaches. Salmonella-induced inflammation suppressed Alistipes and other dominant members, while rarer commensals like Lactobacillus and Enterococcus endure. The rare and novel species sampled across this inflammation gradient advance the utility of this microbiome resource to benefit the broad research needs of the CBA/J scientific community, and those using murine models for understanding the impact of inflammation on the gut microbiome more generally. Video Abstract.
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Affiliation(s)
- Ikaia Leleiwi
- Department of Cell and Molecular Biology, The Colorado State University, Fort Collins, CO USA
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Josué Rodriguez-Ramos
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
- Graduate Degree Program in Ecology, The Colorado State University, Fort Collins, CO USA
| | - Michael Shaffer
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Anice Sabag-Daigle
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH USA
| | - Katherine Kokkinias
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
- Department of Microbiology, Immunology, and Pathology, The Colorado State University, Fort Collins, CO USA
| | - Rory M. Flynn
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Rebecca A. Daly
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Linnea F. M. Kop
- Department of Microbiology, RIBES, Radbound University, Nijmegen, The Netherlands
- Department of Microbiology and Biophysics, The Ohio State University, Columbus, OH USA
| | - Lindsey M. Solden
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Brian M. M. Ahmer
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH USA
| | - Mikayla A. Borton
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
| | - Kelly C. Wrighton
- Department of Cell and Molecular Biology, The Colorado State University, Fort Collins, CO USA
- Department of Soil and Crop Sciences, The Colorado State University, Fort Collins, CO USA
- Graduate Degree Program in Ecology, The Colorado State University, Fort Collins, CO USA
- Department of Microbiology, Immunology, and Pathology, The Colorado State University, Fort Collins, CO USA
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Smid M, Schmidt MK, Prager-van der Smissen WJC, Ruigrok-Ritstier K, Schreurs MAC, Cornelissen S, Garcia AM, Broeks A, Timmermans AM, Trapman-Jansen AMAC, Collée JM, Adank MA, Hooning MJ, Martens JWM, Hollestelle A. Breast cancer genomes from CHEK2 c.1100delC mutation carriers lack somatic TP53 mutations and display a unique structural variant size distribution profile. Breast Cancer Res 2023; 25:53. [PMID: 37161532 PMCID: PMC10169359 DOI: 10.1186/s13058-023-01653-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/02/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND CHEK2 c.1100delC was the first moderate-risk breast cancer (BC) susceptibility allele discovered. Despite several genomic, transcriptomic and functional studies, however, it is still unclear how exactly CHEK2 c.1100delC promotes tumorigenesis. Since the mutational landscape of a tumor reflects the processes that have operated on its development, the aim of this study was to uncover the somatic genomic landscape of CHEK2-associated BC. METHODS We sequenced primary BC (pBC) and normal genomes of 20 CHEK2 c.1100delC mutation carriers as well as their pBC transcriptomes. Including pre-existing cohorts, we exhaustively compared CHEK2 pBC genomes to those from BRCA1/2 mutation carriers, those that displayed homologous recombination deficiency (HRD) and ER- and ER+ pBCs, totaling to 574 pBC genomes. Findings were validated in 517 metastatic BC genomes subdivided into the same subgroups. Transcriptome data from 168 ER+ pBCs were used to derive a TP53-mutant gene expression signature and perform cluster analysis with CHEK2 BC transcriptomes. Finally, clinical outcome of CHEK2 c.1100delC carriers was compared with BC patients displaying somatic TP53 mutations in two well-described retrospective cohorts totaling to 942 independent pBC cases. RESULTS BC genomes from CHEK2 mutation carriers were most similar to ER+ BC genomes and least similar to those of BRCA1/2 mutation carriers in terms of tumor mutational burden as well as mutational signatures. Moreover, CHEK2 BC genomes did not show any evidence of HRD. Somatic TP53 mutation frequency and the size distribution of structural variants (SVs), however, were different compared to ER+ BC. Interestingly, BC genomes with bi-allelic CHEK2 inactivation lacked somatic TP53 mutations and transcriptomic analysis indicated a shared biology with TP53 mutant BC. Moreover, CHEK2 BC genomes had an increased frequency of > 1 Mb deletions, inversions and tandem duplications with peaks at specific sizes. The high chromothripsis frequency among CHEK2 BC genomes appeared, however, not associated with this unique SV size distribution profile. CONCLUSIONS CHEK2 BC genomes are most similar to ER+ BC genomes, but display unique features that may further unravel CHEK2-driven tumorigenesis. Increased insight into this mechanism could explain the shorter survival of CHEK2 mutation carriers that is likely driven by intrinsic tumor aggressiveness rather than endocrine resistance.
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Affiliation(s)
- Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Maartje A C Schreurs
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Sten Cornelissen
- Core Facility Molecular Pathology & Biobanking, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Aida Marsal Garcia
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Annegien Broeks
- Core Facility Molecular Pathology & Biobanking, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - A Mieke Timmermans
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | | | - J Margriet Collée
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Muriel A Adank
- Family Cancer Clinic, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Maartje J Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Antoinette Hollestelle
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands.
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Punyasu N, Kalapanulak S, Saithong T. CO 2 recycling by phospho enolpyruvate carboxylase enables cassava leaf metabolism to tolerate low water availability. FRONTIERS IN PLANT SCIENCE 2023; 14:1159247. [PMID: 37229106 PMCID: PMC10204807 DOI: 10.3389/fpls.2023.1159247] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/12/2023] [Indexed: 05/27/2023]
Abstract
Cassava is a staple crop that acclimatizes well to dry weather and limited water availability. The drought response mechanism of quick stomatal closure observed in cassava has no explicit link to the metabolism connecting its physiological response and yield. Here, a genome-scale metabolic model of cassava photosynthetic leaves (leaf-MeCBM) was constructed to study on the metabolic response to drought and stomatal closure. As demonstrated by leaf-MeCBM, leaf metabolism reinforced the physiological response by increasing the internal CO2 and then maintaining the normal operation of photosynthetic carbon fixation. We found that phosphoenolpyruvate carboxylase (PEPC) played a crucial role in the accumulation of the internal CO2 pool when the CO2 uptake rate was limited during stomatal closure. Based on the model simulation, PEPC mechanistically enhanced drought tolerance in cassava by providing sufficient CO2 for carbon fixation by RuBisCO, resulting in high production of sucrose in cassava leaves. The metabolic reprogramming decreased leaf biomass production, which may lead to maintaining intracellular water balance by reducing the overall leaf area. This study indicates the association of metabolic and physiological responses to enhance tolerance, growth, and production of cassava in drought conditions.
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Affiliation(s)
- Nattharat Punyasu
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, and School of Information Technology, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
| | - Saowalak Kalapanulak
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, and School of Information Technology, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
| | - Treenut Saithong
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, and School of Information Technology, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi (Bang Khun Thian), Bangkok, Thailand
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36
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Grüttner J, van Rijn JM, Geiser P, Florbrant A, Webb DL, Hellström PM, Sundbom M, Sellin ME, Svärd SG. Trophozoite fitness dictates the intestinal epithelial cell response to Giardia intestinalis infection. PLoS Pathog 2023; 19:e1011372. [PMID: 37141303 DOI: 10.1371/journal.ppat.1011372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 05/16/2023] [Accepted: 04/18/2023] [Indexed: 05/06/2023] Open
Abstract
Giardia intestinalis is a non-invasive, protozoan parasite infecting the upper small intestine of most mammals. Symptomatic infections cause the diarrhoeal disease giardiasis in humans and animals, but at least half of the infections are asymptomatic. However, the molecular underpinnings of these different outcomes of the infection are still poorly defined. Here, we studied the early transcriptional response to G. intestinalis trophozoites, the disease-causing life-cycle stage, in human enteroid-derived, 2-dimensional intestinal epithelial cell (IEC) monolayers. Trophozoites preconditioned in media that maximise parasite fitness triggered only neglectable inflammatory transcription in the IECs during the first hours of co-incubation. By sharp contrast, "non-fit" or lysed trophozoites induced a vigorous IEC transcriptional response, including high up-regulation of many inflammatory cytokines and chemokines. Furthermore, "fit" trophozoites could even suppress the stimulatory effect of lysed trophozoites in mixed infections, suggesting active G. intestinalis suppression of the IEC response. By dual-species RNA-sequencing, we defined the IEC and G. intestinalis gene expression programs associated with these differential outcomes of the infection. Taken together, our results inform on how G. intestinalis infection can lead to such highly variable effects on the host, and pinpoints trophozoite fitness as a key determinant of the IEC response to this common parasite.
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Affiliation(s)
- Jana Grüttner
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Jorik M van Rijn
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Petra Geiser
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Alexandra Florbrant
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Dominic-Luc Webb
- Department of Medical Sciences, Gastroenterology and Hepatology Unit, Uppsala University, Uppsala, Sweden
| | - Per M Hellström
- Department of Medical Sciences, Gastroenterology and Hepatology Unit, Uppsala University, Uppsala, Sweden
| | - Magnus Sundbom
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Mikael E Sellin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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37
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Downie AT, Lefevre S, Illing B, Harris J, Jarrold MD, McCormick MI, Nilsson GE, Rummer JL. Rapid physiological and transcriptomic changes associated with oxygen delivery in larval anemonefish suggest a role in adaptation to life on hypoxic coral reefs. PLoS Biol 2023; 21:e3002102. [PMID: 37167194 PMCID: PMC10174562 DOI: 10.1371/journal.pbio.3002102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 03/31/2023] [Indexed: 05/13/2023] Open
Abstract
Connectivity of coral reef fish populations relies on successful dispersal of a pelagic larval phase. Pelagic larvae must exhibit high swimming abilities to overcome ocean and reef currents, but once settling onto the reef, larvae transition to endure habitats that become hypoxic at night. Therefore, coral reef fish larvae must rapidly and dramatically shift their physiology over a short period of time. Taking an integrative, physiological approach, using swimming respirometry, and examining hypoxia tolerance and transcriptomics, we show that larvae of cinnamon anemonefish (Amphiprion melanopus) rapidly transition between "physiological extremes" at the end of their larval phase. Daily measurements of swimming larval anemonefish over their entire early development show that they initially have very high mass-specific oxygen uptake rates. However, oxygen uptake rates decrease midway through the larval phase. This occurs in conjunction with a switch in haemoglobin gene expression and increased expression of myoglobin, cytoglobin, and neuroglobin, which may all contribute to the observed increase in hypoxia tolerance. Our findings indicate that critical ontogenetic changes in the gene expression of oxygen-binding proteins may underpin the physiological mechanisms needed for successful larval recruitment to reefs.
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Affiliation(s)
- Adam T Downie
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia
- School of Biological Sciences, University of Queensland, St. Lucia, Australia
| | - Sjannie Lefevre
- Section for Physiology and Cell Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Björn Illing
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia
- Thünen Institute of Fisheries Ecology, Bremerhaven, Germany
| | - Jessica Harris
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia
| | - Michael D Jarrold
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia
- College of Science and Engineering, James Cook University, Townsville, Australia
| | - Mark I McCormick
- Coastal Marine Field Station, School of Science, University of Waikato, Tauranga, New Zealand
| | - Göran E Nilsson
- Section for Physiology and Cell Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Jodie L Rummer
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Australia
- College of Science and Engineering, James Cook University, Townsville, Australia
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38
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MacPherson RA, Shankar V, Anholt RRH, Mackay TFC. Genetic and Genomic Analyses of Drosophila melanogaster Models of Chromatin Modification Disorders. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.30.534923. [PMID: 37034595 PMCID: PMC10081333 DOI: 10.1101/2023.03.30.534923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Switch/Sucrose Non-Fermentable (SWI/SNF)-related intellectual disability disorders (SSRIDDs) and Cornelia de Lange syndrome are rare syndromic neurodevelopmental disorders with overlapping clinical phenotypes. SSRIDDs are associated with the BAF (Brahma-Related Gene-1 Associated Factor) complex, whereas CdLS is a disorder of chromatin modification associated with the cohesin complex. Here, we used RNA interference in Drosophila melanogaster to reduce expression of six genes (brm, osa, Snr1, SMC1, SMC3, vtd) orthologous to human genes associated with SSRIDDs and CdLS. These fly models exhibit changes in sleep, activity, startle behavior (a proxy for sensorimotor integration) and brain morphology. Whole genome RNA sequencing identified 9,657 differentially expressed genes (FDR < 0.05), 156 of which are differentially expressed in both sexes in SSRIDD- and CdLS-specific analyses, including Bap60, which is orthologous to SMARCD1, a SSRIDD-associated BAF component, k-means clustering reveals genes co-regulated within and across SSRIDD and CdLS fly models. RNAi-mediated reduction of expression of six genes co-regulated with focal genes brm, osa, and/or Snr1 recapitulated changes in behavior of the focal genes. Based on the assumption that fundamental biological processes are evolutionarily conserved, Drosophila models can be used to understand underlying molecular effects of variants in chromatin-modification pathways and may aid in discovery of drugs that ameliorate deleterious phenotypic effects.
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Affiliation(s)
- Rebecca A. MacPherson
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Vijay Shankar
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Robert R. H. Anholt
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Trudy F. C. Mackay
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
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Bairakdar MD, Tewari A, Truttmann MC. A meta-analysis of RNA-Seq studies to identify novel genes that regulate aging. Exp Gerontol 2023; 173:112107. [PMID: 36731807 PMCID: PMC10653729 DOI: 10.1016/j.exger.2023.112107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 02/04/2023]
Abstract
Aging is a ubiquitous biological process that limits the maximal lifespan of most organisms. Significant efforts by many groups have identified mechanisms that, when triggered by natural or artificial stimuli, are sufficient to either enhance or decrease maximal lifespan. Previous aging studies using the nematode Caenorhabditis elegans (C. elegans) generated a wealth of publicly available transcriptomics datasets linking changes in gene expression to lifespan regulation. However, a comprehensive comparison of these datasets across studies in the context of aging biology is missing. Here, we carry out a systematic meta-analysis of over 1200 bulk RNA sequencing (RNASeq) samples obtained from 74 peer-reviewed publications on aging-related transcriptomic changes in C. elegans. Using both differential expression analyses and machine learning approaches, we mine the pooled data for novel pro-longevity genes. We find that both approaches identify known and propose novel pro-longevity genes. Further, we find that inter-lab experimental variance complicates the application of machine learning algorithms, a limitation that was not solved using bulk RNA-Seq batch correction and normalization techniques. Taken as a whole, our results indicate that machine learning approaches may hold promise for the identification of genes that regulate aging but will require more sophisticated batch correction strategies or standardized input data to reliably identify novel pro-longevity genes.
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Affiliation(s)
- Mohamad D Bairakdar
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ambuj Tewari
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI 48109, USA; Department of Statistics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthias C Truttmann
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, 48109, USA; Geriatrics Center, University of Michigan, Ann Arbor, MI 48109, USA.
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40
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Mokashi SS, Shankar V, Johnstun JA, Mackay TFC, Anholt RRH. Pleiotropic fitness effects of a Drosophila odorant-binding protein. G3 (BETHESDA, MD.) 2023; 13:jkac307. [PMID: 36454098 PMCID: PMC9911060 DOI: 10.1093/g3journal/jkac307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 12/05/2022]
Abstract
Insect odorant-binding proteins (OBPs) are members of a rapidly evolving multigene family traditionally thought to facilitate chemosensation. However, studies on Drosophila have shown that members of this family have evolved functions beyond chemosensation, as evident from their expression in reproductive tissues and the brain. Previous studies implicated diverse functions of Obp56h, a member of the largest gene cluster of the D. melanogaster Obp repertoire. Here, we examined the effect of CRISPR/Cas9-mediated deletion of Obp56h on 2 fitness phenotypes, on resistance to starvation stress and heat stress, and on locomotion and sleep phenotypes. Obp56h-/- mutants show a strong sexually dimorphic effect on starvation stress survival, with females being more resistant to starvation stress than the control. In contrast, Obp56h-/- females, but not males, are highly sensitive to heat stress. Both sexes show changes in locomotion and sleep patterns. Transcriptional profiling of RNA from heads of Obp56h-/- flies and the wildtype control reveals differentially expressed genes, including gene products associated with antimicrobial immune responses and members of the Turandot family of stress-induced secreted peptides. In addition, differentially expressed genes of unknown function were identified in both sexes. Genes encoding components of the mitochondrial electron transport chain, cuticular proteins, gene products associated with regulation of feeding behavior (Lst and CCHa2), ribosomal proteins, lncRNAs, snoRNAs, tRNAs, and snRNAs show changes in transcript abundances in Obp56h-/- females. These differentially expressed genes are likely to contribute to Obp56h-mediated effects on the diverse phenotypes that arise upon deletion of this OBP.
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Affiliation(s)
- Sneha S Mokashi
- Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Vijay Shankar
- Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Joel A Johnstun
- Department of Biological Sciences, Program in Genetics, North Carolina State University, Raleigh, NC 27695, USA
| | - Trudy F C Mackay
- Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Robert R H Anholt
- Department of Genetics and Biochemistry and Center for Human Genetics, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
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41
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Ma J, Zhang L, Shen F, Geng Y, Huang Y, Wu H, Fan Z, Hou R, Song Z, Yue B, Zhang X. Gene expressions between obligate bamboo-eating pandas and non-herbivorous mammals reveal converged specialized bamboo diet adaptation. BMC Genomics 2023; 24:23. [PMID: 36647013 PMCID: PMC9843897 DOI: 10.1186/s12864-023-09111-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND It is inevitable to change the function or expression of genes during the environmental adaption of species. Both the giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens) belong to Carnivora and have developed similar adaptations to the same dietary switch to bamboos at the morphological and genomic levels. However, the genetic adaptation at the gene expression level is unclear. Therefore, we aimed to examine the gene expression patterns of giant and red panda convergent specialized bamboo-diets. We examined differences in liver and pancreas transcriptomes between the two panda species and other non-herbivorous species. RESULTS The clustering and PCA plots suggested that the specialized bamboo diet may drive similar expression shifts in these two species of pandas. Therefore, we focused on shared liver and pancreas DEGs (differentially expressed genes) in the giant and red panda relative to other non-herbivorous species. Genetic convergence occurred at multiple levels spanning carbohydrate metabolism, lipid metabolism, and lysine degradation. The shared adaptive convergence DEGs in both organs probably be an evolutionary response to the high carbohydrate, low lipid and lysine bamboo diet. Convergent expression of those nutrient metabolism-related genes in both pandas was an intricate process and subjected to multi-level regulation, including DNA methylation and transcription factor. A large number of lysine degradation and lipid metabolism related genes were hypermethylated in promoter regions in the red panda. Most genes related to carbohydrate metabolism had reduced DNA methylation with increased mRNA expression in giant pandas. Unlike the red panda, the core gene of the lysine degradation pathway (AASS) doesn't exhibit hypermethylation modification in the giant panda, and dual-luciferase reporter assay showed that transcription factor, NR3C1, functions as a transcriptional activator in AASS transcription through the binding to AASS promoter region. CONCLUSIONS Our results revealed the adaptive expressions and regulations of the metabolism-related genes responding to the unique nutrients in bamboo food and provided data accumulation and research hints for the future revelation of complex mechanism of two pandas underlying convergent adaptation to a specialized bamboo diet.
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Affiliation(s)
- Jinnan Ma
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China ,grid.410739.80000 0001 0723 6903College of Continuing Education, Yunnan Normal University, Kunming, 650092 China
| | - Liang Zhang
- grid.452857.9The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081 China
| | - Fujun Shen
- grid.452857.9The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081 China
| | - Yang Geng
- grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China
| | - Yan Huang
- China Conservation and Research Center for the Giant Panda, Wolong, 623006 Sichuan China
| | - Honglin Wu
- China Conservation and Research Center for the Giant Panda, Wolong, 623006 Sichuan China
| | - Zhenxin Fan
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China ,grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China
| | - Rong Hou
- grid.452857.9The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, 610081 China
| | - Zhaobin Song
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China ,grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China
| | - Bisong Yue
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China ,grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China
| | - Xiuyue Zhang
- grid.13291.380000 0001 0807 1581Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China ,grid.13291.380000 0001 0807 1581Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, Chengdu, 610065 China
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Escorcia-Rodríguez JM, Gaytan-Nuñez E, Hernandez-Benitez EM, Zorro-Aranda A, Tello-Palencia MA, Freyre-González JA. Improving gene regulatory network inference and assessment: The importance of using network structure. Front Genet 2023; 14:1143382. [PMID: 36926589 PMCID: PMC10012345 DOI: 10.3389/fgene.2023.1143382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/20/2023] [Indexed: 03/03/2023] Open
Abstract
Gene regulatory networks are graph models representing cellular transcription events. Networks are far from complete due to time and resource consumption for experimental validation and curation of the interactions. Previous assessments have shown the modest performance of the available network inference methods based on gene expression data. Here, we study several caveats on the inference of regulatory networks and methods assessment through the quality of the input data and gold standard, and the assessment approach with a focus on the global structure of the network. We used synthetic and biological data for the predictions and experimentally-validated biological networks as the gold standard (ground truth). Standard performance metrics and graph structural properties suggest that methods inferring co-expression networks should no longer be assessed equally with those inferring regulatory interactions. While methods inferring regulatory interactions perform better in global regulatory network inference than co-expression-based methods, the latter is better suited to infer function-specific regulons and co-regulation networks. When merging expression data, the size increase should outweigh the noise inclusion and graph structure should be considered when integrating the inferences. We conclude with guidelines to take advantage of inference methods and their assessment based on the applications and available expression datasets.
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Affiliation(s)
- Juan M Escorcia-Rodríguez
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Estefani Gaytan-Nuñez
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Undergraduate Program in Genomic Sciences, Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ericka M Hernandez-Benitez
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Undergraduate Program in Genomic Sciences, Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Andrea Zorro-Aranda
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Department of Chemical Engineering, Universidad de Antioquia, Medellín, Colombia
| | - Marco A Tello-Palencia
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Undergraduate Program in Genomic Sciences, Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Julio A Freyre-González
- Regulatory Systems Biology Research Group, Program of Systems Biology, Center for Genomic Sciences, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Cope KR, Prates ET, Miller JI, Demerdash ON, Shah M, Kainer D, Cliff A, Sullivan KA, Cashman M, Lane M, Matthiadis A, Labbé J, Tschaplinski TJ, Jacobson DA, Kalluri UC. Exploring the role of plant lysin motif receptor-like kinases in regulating plant-microbe interactions in the bioenergy crop Populus. Comput Struct Biotechnol J 2022; 21:1122-1139. [PMID: 36789259 PMCID: PMC9900275 DOI: 10.1016/j.csbj.2022.12.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 12/18/2022] [Accepted: 12/30/2022] [Indexed: 01/02/2023] Open
Abstract
For plants, distinguishing between mutualistic and pathogenic microbes is a matter of survival. All microbes contain microbe-associated molecular patterns (MAMPs) that are perceived by plant pattern recognition receptors (PRRs). Lysin motif receptor-like kinases (LysM-RLKs) are PRRs attuned for binding and triggering a response to specific MAMPs, including chitin oligomers (COs) in fungi, lipo-chitooligosaccharides (LCOs), which are produced by mycorrhizal fungi and nitrogen-fixing rhizobial bacteria, and peptidoglycan in bacteria. The identification and characterization of LysM-RLKs in candidate bioenergy crops including Populus are limited compared to other model plant species, thus inhibiting our ability to both understand and engineer microbe-mediated gains in plant productivity. As such, we performed a sequence analysis of LysM-RLKs in the Populus genome and predicted their function based on phylogenetic analysis with known LysM-RLKs. Then, using predictive models, molecular dynamics simulations, and comparative structural analysis with previously characterized CO and LCO plant receptors, we identified probable ligand-binding sites in Populus LysM-RLKs. Using several machine learning models, we predicted remarkably consistent binding affinity rankings of Populus proteins to CO. In addition, we used a modified Random Walk with Restart network-topology based approach to identify a subset of Populus LysM-RLKs that are functionally related and propose a corresponding signal transduction cascade. Our findings provide the first look into the role of LysM-RLKs in Populus-microbe interactions and establish a crucial jumping-off point for future research efforts to understand specificity and redundancy in microbial perception mechanisms.
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Affiliation(s)
- Kevin R. Cope
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Erica T. Prates
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - John I. Miller
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Omar N.A. Demerdash
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Manesh Shah
- Genome Science and Technology, The University of Tennessee–Knoxville, Knoxville, TN 37996, USA
| | - David Kainer
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Ashley Cliff
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville 37996, USA
| | - Kyle A. Sullivan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Mikaela Cashman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Matthew Lane
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville 37996, USA
| | - Anna Matthiadis
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jesse Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | | | - Daniel A. Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA,The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville 37996, USA
| | - Udaya C. Kalluri
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA,Corresponding author.
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Li Y, Gao H, Zhang H, Yu R, Feng F, Tang J, Li B. Characterization and expression profiling of G protein-coupled receptors (GPCRs) in Spodoptera litura (Lepidoptera: Noctuidae). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 44:101018. [PMID: 35994891 DOI: 10.1016/j.cbd.2022.101018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 01/27/2023]
Abstract
Spodoptera litura is a highly destructive omnivorous pest, and they caused serious damage to various crops. G protein-coupled receptors (GPCRs) mediate dozens of physiological processes including reproduction, development, life span and behaviors, but the information of these receptors has been lacking in S. litura. Here, we methodically identified 122 GPCRs in S. litura and made an assay of their expression patterns in different tissues. Comparing the identified GPCRs with homologous genes of other insects, it is obvious that the subfamily A2 (biogenic amine receptors) and the subfamily A3 (neuropeptide and protein hormone receptors) of S. litura have expanded to a certain extent, which may be related to the omnivorous nature and drought environment resistance of S. litura. Besides, the large Methuselah (Mth)/Methuselah-like (Mthl) subfamily of S. litura may be involved in many physiological functions such as longevity and stress response. Apart from duplicate receptors, the loss of parathyroid hormone receptor (PTHR) and the bride of sevenless (Boss) receptor in the lepidopteran insects may imply a new pattern of wing formation and energy metabolism in lepidopteran insects. In addition, the high expression level of GPCRs in different tissues reflects the functional diversity of GPCRs regulating. Systemic identification and initial characterization of GPCRs in S. litura provide a basis for further studies to reveal the functions of these receptors in regulating physiology and behavior.
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Affiliation(s)
- Yanxiao Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Han Gao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Hui Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Runnan Yu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Fan Feng
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Jing Tang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Bin Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
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MacPherson RA, Shankar V, Sunkara LT, Hannah RC, Campbell MR, Anholt RRH, Mackay TFC. Pleiotropic fitness effects of the lncRNA Uhg4 in Drosophila melanogaster. BMC Genomics 2022; 23:781. [PMID: 36451091 PMCID: PMC9710044 DOI: 10.1186/s12864-022-08972-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/26/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) are a diverse class of RNAs that are critical for gene regulation, DNA repair, and splicing, and have been implicated in development, stress response, and cancer. However, the functions of many lncRNAs remain unknown. In Drosophila melanogaster, U snoRNA host gene 4 (Uhg4) encodes an antisense long noncoding RNA that is host to seven small nucleolar RNAs (snoRNAs). Uhg4 is expressed ubiquitously during development and in all adult tissues, with maximal expression in ovaries; however, it has no annotated function(s). RESULTS We used CRISPR-Cas9 germline gene editing to generate multiple deletions spanning the promoter region and first exon of Uhg4. Females showed arrested egg development and both males and females were sterile. In addition, Uhg4 deletion mutants showed delayed development and decreased viability, and changes in sleep and responses to stress. Whole-genome RNA sequencing of Uhg4 deletion flies and their controls identified co-regulated genes and genetic interaction networks associated with Uhg4. Gene ontology analyses highlighted a broad spectrum of biological processes, including regulation of transcription and translation, morphogenesis, and stress response. CONCLUSION Uhg4 is a lncRNA essential for reproduction with pleiotropic effects on multiple fitness traits.
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Affiliation(s)
- Rebecca A MacPherson
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC, 29646, USA
| | - Vijay Shankar
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC, 29646, USA
| | - Lakshmi T Sunkara
- Present adress: Clemson Veterinary Diagnostic Center, Livestock Poultry Health, Clemson University, 500 Clemson Road, Columbia, SC, 29229, USA
| | - Rachel C Hannah
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC, 29646, USA
| | - Marion R Campbell
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC, 29646, USA
| | - Robert R H Anholt
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC, 29646, USA.
| | - Trudy F C Mackay
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC, 29646, USA.
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46
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Zatzman M, Fuligni F, Ripsman R, Suwal T, Comitani F, Edward LM, Denroche R, Jang GH, Notta F, Gallinger S, Selvanathan SP, Toretsky JA, Hellmann MD, Tabori U, Huang A, Shlien A. Widespread hypertranscription in aggressive human cancers. SCIENCE ADVANCES 2022; 8:eabn0238. [PMID: 36417526 PMCID: PMC9683723 DOI: 10.1126/sciadv.abn0238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 10/07/2022] [Indexed: 05/10/2023]
Abstract
Cancers are often defined by the dysregulation of specific transcriptional programs; however, the importance of global transcriptional changes is less understood. Hypertranscription is the genome-wide increase in RNA output. Hypertranscription's prevalence, underlying drivers, and prognostic significance are undefined in primary human cancer. This is due, in part, to limitations of expression profiling methods, which assume equal RNA output between samples. Here, we developed a computational method to directly measure hypertranscription in 7494 human tumors, spanning 31 cancer types. Hypertranscription is ubiquitous across cancer, especially in aggressive disease. It defines patient subgroups with worse survival, even within well-established subtypes. Our data suggest that loss of transcriptional suppression underpins the hypertranscriptional phenotype. Single-cell analysis reveals hypertranscriptional clones, which dominate transcript production regardless of their size. Last, patients with hypertranscribed mutations have improved response to immune checkpoint therapy. Our results provide fundamental insights into gene dysregulation across human cancers and may prove useful in identifying patients who would benefit from novel therapies.
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Affiliation(s)
- Matthew Zatzman
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Fabio Fuligni
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ryan Ripsman
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tannu Suwal
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Federico Comitani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Lisa-Monique Edward
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rob Denroche
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gun Ho Jang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Faiyaz Notta
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Steven Gallinger
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Wallace McCain Centre for Pancreatic Cancer, Department of Medical Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Ontario, Canada
| | | | - Jeffrey A. Toretsky
- Departments of Oncology and Pediatrics, Georgetown University, Washington, DC 20057, USA
| | - Matthew D. Hellmann
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Uri Tabori
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Annie Huang
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Adam Shlien
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
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Aubé J, Cambon-Bonavita MA, Velo-Suárez L, Cueff-Gauchard V, Lesongeur F, Guéganton M, Durand L, Reveillaud J. A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata. MICROBIOME 2022; 10:189. [PMID: 36333777 PMCID: PMC9636832 DOI: 10.1186/s40168-022-01380-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND In deep-sea hydrothermal vent areas, deprived of light, most animals rely on chemosynthetic symbionts for their nutrition. These symbionts may be located on their cuticle, inside modified organs, or in specialized cells. Nonetheless, many of these animals have an open and functional digestive tract. The vent shrimp Rimicaris exoculata is fueled mainly by its gill chamber symbionts, but also has a complete digestive system with symbionts. These are found in the shrimp foregut and midgut, but their roles remain unknown. We used genome-resolved metagenomics on separate foregut and midgut samples, taken from specimens living at three contrasted sites along the Mid-Atlantic Ridge (TAG, Rainbow, and Snake Pit) to reveal their genetic potential. RESULTS We reconstructed and studied 20 Metagenome-Assembled Genomes (MAGs), including novel lineages of Hepatoplasmataceae and Deferribacteres, abundant in the shrimp foregut and midgut, respectively. Although the former showed streamlined reduced genomes capable of using mostly broken-down complex molecules, Deferribacteres showed the ability to degrade complex polymers, synthesize vitamins, and encode numerous flagellar and chemotaxis genes for host-symbiont sensing. Both symbionts harbor a diverse set of immune system genes favoring holobiont defense. In addition, Deferribacteres were observed to particularly colonize the bacteria-free ectoperitrophic space, in direct contact with the host, elongating but not dividing despite possessing the complete genetic machinery necessary for this. CONCLUSION Overall, these data suggest that these digestive symbionts have key communication and defense roles, which contribute to the overall fitness of the Rimicaris holobiont. Video Abstract.
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Affiliation(s)
- Johanne Aubé
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Marie-Anne Cambon-Bonavita
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Lourdes Velo-Suárez
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
- Univ Brest, INSERM, EFS, UMR 1078, GGB, F-29200 Brest, France and Centre Brestois d’Analyse du Microbiote (CBAM), Brest University Hospital, Brest, France
| | - Valérie Cueff-Gauchard
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Françoise Lesongeur
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Marion Guéganton
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Lucile Durand
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
| | - Julie Reveillaud
- Univ Brest, CNRS, Ifremer, UMR6197 Biologie et Ecologie des Ecosystèmes marins Profonds, F-29280 Plouzané, France
- MIVEGEC, Univ. Montpellier, INRAe, CNRS, IRD, Montpellier, France
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Michelotti TC, Kisby BR, Flores LS, Tegeler AP, Fokar M, Crasto C, Menarim BC, Loux SC, Strieder-Barboza C. Single-nuclei analysis reveals depot-specific transcriptional heterogeneity and depot-specific cell types in adipose tissue of dairy cows. Front Cell Dev Biol 2022; 10:1025240. [PMID: 36313560 PMCID: PMC9616121 DOI: 10.3389/fcell.2022.1025240] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
Adipose tissue (AT) is an endocrine organ with a central role on whole-body energy metabolism and development of metabolic diseases. Single-cell and single-nuclei RNA sequencing (scRNA-seq and snRNA-seq, respectively) analyses in mice and human AT have revealed vast cell heterogeneity and functionally distinct subtypes that are potential therapeutic targets to metabolic disease. In periparturient dairy cows, AT goes through intensive remodeling and its dysfunction is associated with metabolic disease pathogenesis and decreased productive performance. The contributions of depot-specific cells and subtypes to the development of diseases in dairy cows remain to be studied. Our objective was to elucidate differences in cellular diversity of visceral (VAT) and subcutaneous (SAT) AT in dairy cows at the single-nuclei level. We collected matched SAT and VAT samples from three dairy cows and performed snRNA-seq analysis. We identified distinct cell types including four major mature adipocytes (AD) and three stem and progenitor cells (ASPC) subtypes, along with endothelial cells (EC), mesothelial cells (ME), immune cells, and pericytes and smooth muscle cells. All major cell types were present in both SAT and VAT, although a strong VAT-specificity was observed for ME, which were basically absent in SAT. One ASPC subtype was defined as adipogenic (PPARG+) while the other two had a fibro-adipogenic profile (PDGFRA+). We identified vascular and lymphatic EC subtypes, and different immune cell types and subtypes in both SAT and VAT, i.e., macrophages, monocytes, T cells, and natural killer cells. Not only did VAT show a greater proportion of immune cells, but these visceral immune cells had greater activation of pathways related to immune and inflammatory response, and complement cascade in comparison with SAT. There was a substantial contrast between depots for gene expression of complement cascade, which were greatly expressed by VAT cell subtypes compared to SAT, indicating a pro-inflammatory profile in VAT. Unprecedently, our study demonstrated cell-type and depot-specific heterogeneity in VAT and SAT of dairy cows. A better understanding of depot-specific molecular and cellular features of SAT and VAT will aid in the development of AT-targeted strategies to prevent and treat metabolic disease in dairy cows, especially during the periparturient period.
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Affiliation(s)
- Tainara C. Michelotti
- Department of Veterinary Sciences, Davis College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX, United States
| | - Brent R. Kisby
- Department of Pharmacology and Neuroscience, Texas Tech University Health Science Center, Lubbock, TX, United States
| | - Lauryn S. Flores
- Department of Veterinary Sciences, Davis College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX, United States
| | - Alexandra P. Tegeler
- Department of Veterinary Sciences, Davis College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX, United States
| | - Mohamed Fokar
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, United States
| | - Chiquito Crasto
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, United States
- Department of Computer Science, Whitacre College of Engineering, Texas Tech University, Lubbock, TX, United States
- Department of University Studies, Texas Tech University, Lubbock, TX, United States
| | - Bruno C. Menarim
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, United States
| | - Shavahn C. Loux
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, United States
| | - Clarissa Strieder-Barboza
- Department of Veterinary Sciences, Davis College of Agricultural Sciences and Natural Resources, Texas Tech University, Lubbock, TX, United States
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX, United States
- *Correspondence: Clarissa Strieder-Barboza,
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Influence of African Swine Fever Virus on Host Gene Transcription within Peripheral Blood Mononuclear Cells from Infected Pigs. Viruses 2022; 14:v14102147. [PMID: 36298701 PMCID: PMC9610944 DOI: 10.3390/v14102147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/26/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
African swine fever virus (ASFV) has become a global threat to the pig production industry and has caused enormous economic losses in many countries in recent years. Peripheral blood mononuclear cells (PBMCs) from pigs infected with ASFV not only express ASFV genes (almost 200 in number) but have altered patterns of host gene expression as well. Both up- and down-regulation of host cell gene expression can be followed using RNAseq on poly(A)+ mRNAs harvested from the PBMCs of pigs collected at different times post-infection. Consistent with the time course of changes in viral gene expression, only few and limited changes in host gene expression were detected at 3 days post-infection (dpi), but by 6 dpi, marked changes in the expression of over 1300 host genes were apparent. This was co-incident with the major increase in viral gene expression. The majority of the changes in host gene expression were up-regulation, but many down-regulated genes were also identified. The patterns of changes in gene expression within the PBMCs detected by RNAseq were similar in each of the four infected pigs. Furthermore, changes in the expression of about twenty selected host genes, known to be important in host defence and inflammatory responses, were confirmed using high-throughput microfluidic qPCR assays.
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50
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Nelson AR, Narrowe AB, Rhoades CC, Fegel TS, Daly RA, Roth HK, Chu RK, Amundson KK, Young RB, Steindorff AS, Mondo SJ, Grigoriev IV, Salamov A, Borch T, Wilkins MJ. Wildfire-dependent changes in soil microbiome diversity and function. Nat Microbiol 2022; 7:1419-1430. [PMID: 36008619 PMCID: PMC9418001 DOI: 10.1038/s41564-022-01203-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 07/18/2022] [Indexed: 12/13/2022]
Abstract
Forest soil microbiomes have crucial roles in carbon storage, biogeochemical cycling and rhizosphere processes. Wildfire season length, and the frequency and size of severe fires have increased owing to climate change. Fires affect ecosystem recovery and modify soil microbiomes and microbially mediated biogeochemical processes. To study wildfire-dependent changes in soil microbiomes, we characterized functional shifts in the soil microbiota (bacteria, fungi and viruses) across burn severity gradients (low, moderate and high severity) 1 yr post fire in coniferous forests in Colorado and Wyoming, USA. We found severity-dependent increases of Actinobacteria encoding genes for heat resistance, fast growth, and pyrogenic carbon utilization that might enhance post-fire survival. We report that increased burn severity led to the loss of ectomycorrhizal fungi and less tolerant microbial taxa. Viruses remained active in post-fire soils and probably influenced carbon cycling and biogeochemistry via turnover of biomass and ecosystem-relevant auxiliary metabolic genes. Our genome-resolved analyses link post-fire soil microbial taxonomy to functions and reveal the complexity of post-fire soil microbiome activity.
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Affiliation(s)
- Amelia R Nelson
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Adrienne B Narrowe
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
- Eastern Regional Research Center, Agricultural Research Service, Wyndmoor, PA, USA
| | - Charles C Rhoades
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, CO, USA
| | - Timothy S Fegel
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, CO, USA
| | - Rebecca A Daly
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Holly K Roth
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Rosalie K Chu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Kaela K Amundson
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Robert B Young
- Chemical Analysis and Instrumentation Laboratory, New Mexico State University, Las Cruces, NM, USA
| | - Andrei S Steindorff
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Stephen J Mondo
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Igor V Grigoriev
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Asaf Salamov
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Thomas Borch
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, CO, USA
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA.
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